Is it good to leave hyperref activated on a conference paper? It is recommended to send a copy to an IEEE conference with the hyper-references activated?
This includes hyperlinks to sections, equations, tables, references, etc. The paper was written using LaTeX.
Yes, with a caveat: make sure that the hyperrefs don't include any information that can't be gleaned from the text itself. For example, a common mistake is to use \href to hide a URL, as in:
Our tool is available online \href{http://www.github.com/some/repo/}{here}.

This is acceptable on websites but not in a paper because if the paper is printed, the URL is not visible and impossible to recover.
Similarly, this is bad:
As we showed \hypertarget{page1sec2}{earlier}, every Foo Bar is a Foo Baz

since it only displays the text &quot;earlier&quot;, so an offline reader will have trouble following the backward reference.
Generally, tools like cleveref (\Cref / \cref) do a better job of displaying something that is readable both in text and in interactive form.