Is it correct to use citations as nouns for scientific papers, such as dissertations of articles? Which of these two is better accepted, or preferred, for scientific papers?
THIS
The model detaches the calculation of the vertical velocity from the
equations system, and focuses on the longitudinal velocities instead, leaving the model
as a 2D equations system. [Mintgen, 2018] provides a description for the properties, characteristics and limitations of SWE in a detailed manner, some of which will be further addressed an extended for a deeper analysis in Section 2.1.
OR
The model detaches the calculation of the vertical velocity from the
equations system, and focuses on the longitudinal velocities instead, leaving the model
as a 2D equations system. In his dissertation, Florian Mintgen [Mintgen, 2018] provides a description for the properties, characteristics and limitations of SWE in a detailed manner, some of which will be further addressed an extended for a deeper analysis in Section 2.1.
Or if you have any other accepted way of doing it, please feel free. Thank you
References
[Mintgen, 2018] Mintgen, G. F. (2018). Coupling of Shallow and Non-Shallow Flow Solvers An
Open Source Framework. Dissertation, Technische Universitaet Muenchen, Muenchen.
There’s no unique answer to this as citation styles (in text or in bibliography) are somewhat personal or institutional.  Some good ways of getting guidance include

Get one or more previous theses on the same topic and follow those models,
Look up established journals in the field and use their models (if they have a common one).

I personally prefer your second alternative but would then use numbered referencing to avoid name repetition, v.g. “In his dissertation [1], Mintgen ...”