Q:

Author(year) style mixed up with shortand usage

For my thesis I have to write a literature review. Within the review I must use "shorthand" names for cited works like "S001" and "S002" for the first and the second work that will be cited.
In later chapters the Author(year) style has to be used. Unfortunately the two styles will be mixed-up. I did not find a proper solution, anyone that can help?

    \begin{filecontents}{myfilea.bib}
@book{goossens93,
    author    = "Michel Goossens and Frank Mittelbach and Alexander Samarin",
    title     = "The LaTeX Companion",
    year      = "1993",
%    shorthand = "GMS"
}

@book{else2015,
    author    = "Someone Else",
    title     = "Interesting thing.",
    year      = "2015",
    shorthand = "ElseShort",
}

@article{borges2018,
    author = {Borges, M.  and Barros, E.  and Maia, P. H.},
    title = {Cloud restriction solver: A refactoring-based approach to migrate applications to the cloud},
    journal = {Information and Software Technology},
    uuid = {52D09357-6BA8-4CB1-91B8-8C4CDD7E351B},
    volume = {95},
    pages = {346-365},
    shorthand = {S002},
    year = {2018},
}
\end{filecontents}

\documentclass{article}

    \usepackage[automark, draft=false]{scrlayer-scrpage}
    \setcounter{secnumdepth}{3}
    \setcounter{tocdepth}{3}
    \usepackage[utf8]{inputenc}
    \usepackage[T1]{fontenc}
    \usepackage{lmodern}
    \usepackage{mathptmx}
    \usepackage{courier}
    \usepackage[protrusion,factor=900]{microtype}
    \usepackage{setspace}
    \usepackage{printlen}

\usepackage[backend=biber, %% Hilfsprogramm "biber" (statt "biblatex" oder "bibtex")
                style=authoryear, %% Zitierstil: Authorennamen lang [Jahr]
            bibencoding=utf8,
                natbib=true, %% Bereitstellen von natbib-kompatiblen Zitierkommandos
                backref=true, %% Seiten anzeigen, auf denen die Referenz vorkommt
                ibidtracker=context, %% EBENDA-Anzeige bei mehrfachen Zitierungen der selben Quelle auf einer Seite 
                block=space, %% kleiner horizontaler Platz zwischen den Feldern
                isbn=false, %% ISBN nicht anzeigen, gleiches geht mit nahezu allen anderen Feldern
                url=false, %% Url-Feld wird ausgeblendet. Ausnahme: Online-Typ
                pagetracker=true, %% ebd. bei wiederholten Angaben (false=ausgeschaltet, page=Seite, spread=Doppelseite, true=automatisch)
                citetracker=true, % Wird benötigt für kapitelweise Referenzen?
                sorting=nyt, % To get an sorted bibliography
                ]{biblatex}

% "notoccite" prevents cites in captions from misnumbering of references
\usepackage{notoccite}

% ibidem: Wenn Fußnoten mehrfach auf der selben Seite zur selben Quelle führen, so schreibe "ibidem" (=ebenda).
\providecommand*{\mkibid}[1]{#1}
\DeclareCiteCommand{\footpartcite}[\mkbibfootnote]
  {\usebibmacro{prenote}}
  {\usebibmacro{citeindex}%
   \ifthenelse{\ifciteibid\AND\NOT\iffirstonpage}
     {\printtext[bibhyperref]{\bibstring[\mkibid]{ibidem}}}
     {\printtext[brackets]{\usebibmacro{cite}}%
      \setunit{\addnbspace}%
      \printnames{labelname}%
      \setunit{\labelnamepunct}%
      \printfield[citetitle]{title}%
      \newunit
      \printfield{year}}}
  {\multicitedelim}
  {\usebibmacro{postnote}}

%\usepackage[backend=biber,citestyle=authoryear]{biblatex}
\addbibresource{myfilea.bib}

\begin{document}

In my case I want to use the author (year) citation style: \citet{goossens93}.

But something went wrong: When I use shorthand within a bib element, shorthand and the authoryear will be mixed up: \citet{else2015} 

This is only the "shorthand"-style which I need also within my work: \cite{borges2018}. 

And this is the the Author (year) combination -- unfortunately it wrotes the shorthand into the year part!: \citet{borges2018}.

\end{document}

EDIT:
This is what I want to reach:

I add now a new code example:
\begin{filecontents}{myfile.bib}
@book{goossens93,
    author    = "Michel Goossens and Frank Mittelbach and Alexander Samarin",
    title     = "The LaTeX Companion",
    year      = "1993",
%    shorthand = "GMS"
}

@book{else2015,
    author    = "Someone Else",
    title     = "Interesting thing.",
    year      = "2015",
    shorthand = "S003",
}

@article{borges2018,
    author = {Borges, M.  and Barros, E.  and Maia, P. H.},
    title = {Cloud restriction solver: A refactoring-based approach to migrate applications to the cloud},
    journal = {Information and Software Technology},
    uuid = {52D09357-6BA8-4CB1-91B8-8C4CDD7E351B},
    volume = {95},
    pages = {346-365},
    shorthand = {S002},
    year = {2018},
}
\end{filecontents}

\documentclass{article}

    \usepackage[automark, draft=false]{scrlayer-scrpage}
    \setcounter{secnumdepth}{3}
    \setcounter{tocdepth}{3}
    \usepackage[utf8]{inputenc}
    \usepackage[T1]{fontenc}
    \usepackage{lmodern}
    \usepackage{mathptmx}
    \usepackage{courier}
    \usepackage[protrusion,factor=900]{microtype}
    \usepackage{setspace}
    \usepackage{printlen}
\usepackage{longtable} %needed for longtab
\LTchunksize=8 %% Row count for simplify pagebreak for longtabu environment

%% Needed for labelling longtabu!
\usepackage{caption}
\DeclareCaptionLabelSeparator{tableNewline}{\par} 
\captionsetup{
  justification=centering,
  labelsep=quad,
  }
\captionsetup[longtable]{
  justification=centering,
  labelsep=quad,
  }

\usepackage{tabu}
\usepackage{hhline} % Needed for longtabu when two hlines (==) should be drawn.

\usepackage{tabularx}
\usepackage{booktabs} %Professionelle Tabellen

\usepackage[backend=biber, %% Hilfsprogramm "biber" (statt "biblatex" oder "bibtex")
                style=authoryear, %% Zitierstil: Authorennamen lang [Jahr]
            bibencoding=utf8,
                natbib=true, %% Bereitstellen von natbib-kompatiblen Zitierkommandos
                backref=true, %% Seiten anzeigen, auf denen die Referenz vorkommt
                ibidtracker=context, %% EBENDA-Anzeige bei mehrfachen Zitierungen der selben Quelle auf einer Seite 
                block=space, %% kleiner horizontaler Platz zwischen den Feldern
                isbn=false, %% ISBN nicht anzeigen, gleiches geht mit nahezu allen anderen Feldern
                url=false, %% Url-Feld wird ausgeblendet. Ausnahme: Online-Typ
                pagetracker=true, %% ebd. bei wiederholten Angaben (false=ausgeschaltet, page=Seite, spread=Doppelseite, true=automatisch)
                citetracker=true, % Wird benötigt für kapitelweise Referenzen?
                sorting=nyt, % To get an sorted bibliography
                ]{biblatex}

\usepackage[%
% Standard options
final=true,%
pageanchor=true,%
pagebackref=false,%
hyperindex=true,%
hyperfootnotes=true,%
linktocpage=false,%
breaklinks=false,%
colorlinks=true,%
% PDF options
bookmarks=true,
bookmarksopen=true,%
bookmarksopenlevel=1,%
pdfhighlight=/N,%
allbordercolors={0.85 0.85 1},
citebordercolor={1 1 1},
urlbordercolor={1 1 1},%
% PDF entries
pdftitle={\mydoctitle},%
pdfauthor={\myname},%
pdfsubject={\mysubject},%
pdfcreator={Thomas Salzmann},%
pdfproducer={LaTeX},%
pdfkeywords={\mykeywords},%
% PDF misc settings
pdfstartpage=1,% Start PDF Viewer on Page 1
pdfduplex=Simplex,%
pdfpagelabels=true,%
pdfprintscaling=None,%
citecolor=blue,%
filecolor=blue,%
linkcolor=blue,%
urlcolor=black,%
]{hyperref}

% "notoccite" prevents cites in captions from misnumbering of references
\usepackage{notoccite}

\newcommand{\citeNotAsShorthand}[2][blue]{\textcolor{#1}{\citeauthor{#2} (\citeyear{#2}) [\citefield{#2}{shorthand}]}}

% ibidem: Wenn Fußnoten mehrfach auf der selben Seite zur selben Quelle führen, so schreibe "ibidem" (=ebenda).
\providecommand*{\mkibid}[1]{#1}
\DeclareCiteCommand{\footpartcite}[\mkbibfootnote]
  {\usebibmacro{prenote}}
  {\usebibmacro{citeindex}%
   \ifthenelse{\ifciteibid\AND\NOT\iffirstonpage}
     {\printtext[bibhyperref]{\bibstring[\mkibid]{ibidem}}}
     {\printtext[brackets]{\usebibmacro{cite}}%
      \setunit{\addnbspace}%
      \printnames{labelname}%
      \setunit{\labelnamepunct}%
      \printfield[citetitle]{title}%
      \newunit
      \printfield{year}}}
  {\multicitedelim}
  {\usebibmacro{postnote}}

%\usepackage[backend=biber,citestyle=authoryear]{biblatex}
\addbibresource{myfile.bib}

\begin{document}

In my case I want to use the author (year) citation style: \citet{goossens93}.

But something went wrong: When I use shorthand within a bib element, shorthand and the authoryear will be mixed up: \citet{else2015} 

This is only the "shorthand"-style which I need also within my work: \cite{borges2018}. 

And this is the the Author (year) combination -- unfortunately it wrotes the shorthand into the year part!: \citet{borges2018}.

What I want is this version: \citeNotAsShorthand{borges2018}

\begin{longtabu} to \textwidth {| l | X[1.5,l] %aligned left, twice as wide as second column
                                | X[1,l] |} %aligned left

% Table header on first page of table
    \caption{Table of excluded studies during title- and abstract analysis} \tabularnewline  
    \hline %\toprule
    \thead{Study}& \thead{Title of excluded study (year)} & \thead{reason for exclusion} \tabularnewline 
    \hhline{===}
 %\toprule
    \endfirsthead

% Table header on every other page of table
    \caption{Table of excluded studies during title- and abstract analysis (continued)} \tabularnewline          
    \hline %\toprule
    \thead{Study}& \thead{Title of excluded study (year)} & \thead{reason for exclusion} \tabularnewline 
    \hhline{===}
    \endhead
% End of header

% SCOPUS-search new:
\cite{else2015} & \citetitle{else2015} (\citeyear{else2015}) & Primary focus is not on product management. Focus is on side effects of programs from coding perspective.  \tabularnewline 
\cite{borges2018} &  \citetitle{borges2018} (\citeyear{borges2018}) & Grey literature (article in press). \tabularnewline 
\end{longtabu}

\printbiblist[title={List of relevant studies found during literature review},notkeyword=LRexcluded]{shorthand}

\printbibliography[segment=3,heading=subbibliography]

\end{document}

A:

As mentioned in https://github.com/plk/biblatex/issues/569 \textcite/\citet is more than just \cite with parentheses around the year. You will see different behaviour as well if you use pre- and postnotes, compare \cite[cf.][380]{sigfridsson} and \textcite[cf.][380]{sigfridsson}.

The idea is that \textcite is used as the subject of the sentence for cases like \Textcite{sigfridsson} found that .... To make sure that the grammatical structure is the same for all \textcites, it will show Authors (shorthand) if the shorthand field is given.
If you want the usual behaviour of \cite just with parentheses around the year, I suggest you try biblatex-ext and its cite delimiter feature (§5.3 Delimiters for citation commands of the biblatex-ext documentation).
\DeclareInnerCiteDelims{cite}{\bibopenparen}{\bibcloseparen}

should give you what you want.
Furthermore, I think that study IDs are best dealt with via a dedicated field and not with shorthand. So in the example below I created a new field studyid. If there is an algorithmic way to assign the study ID this could be further automated (this could make for a nice follow-up question), at the moment you have to assign the field value manually in the .bib. studyid is declared a label field so that we can use \printbiblist easily.
We define two cite macros \citewid and \citeonlyid. \citewid shows the citation and together with the study ID. \citeonlyid shows only the study ID.
Finally we set up everything needed for \printbiblist.
\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{lmodern}

\usepackage{filecontents}
\begin{filecontents*}{studyid.dbx}
\DeclareDatamodelFields[type=field,datatype=literal,label=true]{studyid}
\DeclareDatamodelEntryfields{studyid}
\end{filecontents*}

\usepackage[backend=biber, style=ext-authoryear, datamodel=studyid]{biblatex}

% \cite should give author (year)
\DeclareInnerCiteDelims{cite}{\bibopenparen}{\bibcloseparen}

% define \citewid: author (year) [study-id]
\RegisterCiteDelims{outer}{citewid}
\RegisterCiteDelims{inner}{citewid}
\DeclareInnerCiteDelimsAlias{citewid}{cite}
\DeclareFieldAlias{extblx@innercitewiddelims}{extblx@innercitedelims}

\DeclareFieldFormat{citestudyid}{\mkbibbrackets{S#1}}

\newbibmacro*{citewid}{%
  \usebibmacro{cite}%
  \setunit{\addspace}%
  \printfield[citestudyid]{studyid}}

\DeclareCiteCommand{\citewid}[\mkoutercitewiddelims]
  {\usebibmacro{prenote}}
  {\usebibmacro{citeindex}%
   \usebibmacro{citewid}}
  {\multicitedelim}
  {\usebibmacro{postnote}}

% define \citeonlyid: [study-id]
\RegisterCiteDelims{outer}{citeonlyid}
\DeclareOuterCiteDelims{citeonlyid}{\bibopenbracket}{\bibclosebracket}
\DeclareCiteCommand{\citeonlyid}[\mkouterciteonlyiddelims]
  {\usebibmacro{prenote}}
  {\iffieldundef{studyid}
     {\PackageWarning{biblatex}{%
      No 'studyid' in entry '\thefield{entrykey}'.\MessageBreak
      Add the 'studyid' field\MessageBreak
      or don't cite this entry with\MessageBreak
      '\string\citeonlyid'}}
     {\printfield[studyidwidth]{studyid}}}
  {\multicitedelim}
  {\usebibmacro{postnote}}

% \printbiblist similar to shorthand definitions
\DeclareBibliographyDriver{studyid}{%
  \usedriver
    {}
    {\thefield{entrytype}}%
  \finentry}

\DeclareFieldFormat{studyidwidth}{S#1}
\defbibenvironment{studyid}
  {\list
     {\printfield[studyidwidth]{studyid}}
     {\setlength{\labelwidth}{\studyidwidth}%
      \setlength{\leftmargin}{\labelwidth}%
      \setlength{\labelsep}{\biblabelsep}%
      \addtolength{\leftmargin}{\labelsep}%
      \setlength{\itemsep}{\bibitemsep}%
      \setlength{\parsep}{\bibparsep}%
      \renewcommand*{\makelabel}[1]{##1\hss}}}
  {\endlist}
  {\item}

\DeclareSortingTemplate{studyid}{
  \sort{
    \field{studyid}
  }
}

\begin{filecontents}{\jobname.bib}
@article{borges2018,
  author    = {Borges, M.  and Barros, E.  and Maia, P. H.},
  title     = {Cloud restriction solver:
               A refactoring-based approach to migrate applications to the cloud},
  journal   = {Information and Software Technology},
  volume    = {95},
  pages     = {346-365},
  year      = {2018},
  studyid   = {002},
}
@article{licht2009,
  author  = {Licht, Carmilla M. M. and de Geus, Eco J. C.
             and van Dyck, Richard and Penninx, Brenda W. J. H.},
  title   = {Association between anxiety disorders and
             heart rate variability in {The} {Netherlands} {Study} of
             {Depression} and {Anxiety} ({NESDA})},
  journal = {Psychosomatic medicine},
  volume  = {71},
  number  = {5},
  pages   = {508--518},
  doi     = {10.1097/PSY.0b013e3181a292a6},
  date    = {2009},
  studyid = {001},
}
\end{filecontents}

\addbibresource{\jobname.bib}
\addbibresource{biblatex-examples.bib}

\begin{document}
\cite{sigfridsson}

\cite{borges2018}

\citewid{borges2018}

\citeonlyid{borges2018,licht2009}

\printbiblist[title=List of studies]{studyid}

\printbibliography
\end{document}

