Shall acronyms in scientific papers be expanded exactly once? There's no way to evade having a lot of acronyms in a scientific paper, often already in the title.

I use the latex package glossaries to automatically expand the first use of every acronym (except usage in the title), but for a scientific paper, I do not include a table of acronyms (for my thesis I do).  In a long paper, if someone does not remember all acronyms or does not read sequentially, it could be difficult to look up the meaning.

If I use a not very well known acronym in, say, line 100, and again in line 500, should I expand it again, or is it a better style to stick with expanding only and exactly once?
First, try to avoid acronyms unless you repeat it frequently. 

In the case you mention, occurring twice, an acronym is not warranted. New acronyms may be useful if it is likely that it will be used over and over again, both in your paper and in subsequent ones. It is difficult to say how many repetitions is needed before an acronym may become a viable option. 

Acronyms generally make a paper less readable. We all know some like DNA or UN and particularly in the first case the acronym is easier to remember than the actual words. So use acronyms sparingly, be careful about what you abbreviate, and avoid publishing acronyms that only your research group uses unless it starts to become a standard (identified by other people also using it in presentations etc.). I think many acronyms start by it becoming jargon first. Trying to be restrictive is the best measure.