Shall acronyms in scientific papers be expanded 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.