You seem to think papers being legible is not important. Fine. Who needs to actually understand what the authors wrote?

But AI is extremely powerful for scientific research, and is massively increasing scientific output. It has side-effects that will have to be dealt with, like an increase in junk submitted to the journals, but there are ways to deal with that (the simplest one would be to use AI to screen out obvious junk).

So no, science is not "shooting itself in the foot." AI is a massive boost for science, but like every new powerful tool, it has side effects. The biggest side-effect in the long term may be that AI does all the work for us, but we haven't crossed that bridge yet.