Novel-like writing style often sacrifices clarity and accessibility, is it ok to use it in scientific texts? In writing, there are many things one can do to make the text better.
Some basic rules of thumb include avoiding repetitions, avoiding passive voice, breaking down long and complicated sentences, or letting the reader think for themselves.

Do such rules also apply to scientific texts, and if not, why?

I can think of a few reasons why they may not.
For example, avoiding repetition may create confusion — it might not be immediately clear if the alternative term is just a synonym, or if it is different and in what way.
Moreover, using more advanced devices (or,  for that matter, sophisticated vocabulary) could be problematic even for native speakers.

Surely we need to make the text as accessible and clear as possible, but it would be great if it were also enjoyable to read.
Where lies the right balance?
Keep in mind that the goals of a nice fictional book are not at all the same as of an academic paper or a thesis. The former is primarily about entertaining or stimulating the reader. The latter is about providing a certain information (the research result) in the clearest way possible.

The "many things one can do to make the text better" that you mention are geared towards making the text easier to read and less of a chore. While this is certainly also valuable for an academic text, being "easy to read" is ultimately a nice-to-have, while clarity and non-ambiguity are absolutely essential. If you keep in mind that clarity absolutely should not be compromised, you will get an impression why academic texts are written the way they are:


  avoiding repetitions


As you say yourself - if you strive for clearness, having multiple names for the same thing is not good at all.


  avoiding passive voice


Academic texts tend to prefer passive voice mostly because the "story" of an academic paper isn't about the writer, it is about the effect that is observed / described. Writing the paper like you are telling your mother what you did the lest 5 years would put the emphasis on you and your experiments, rather than the data and the observed effects.


  breaking down long and complicated sentences


Yes, do that. Even in academic texts. It's just not easy for those of us that don't have English as first language. In German, for instance, you are taught from very early age on that short sentences "sound stupid". This is hard to unlearn.


  letting the reader to think for themselves


You will never want to "let the reader think for himself" in a paper. It's not a piece of art. You want to present the facts and what derives from them as clearly as possible, not write your paper in a fluffy way so that every reader can come to the conclusions that are most suitable to her/him.