My opinion is that Harry's taught enough rationality at Hogwarts that the lie will fall apart.

Not judging by everyone's reactions when Hermione was accused of murder. A select few individuals might manage to question it at best.

Now that I think about it, shouldn't some Hogwarts students and/or teachers have figured out that they should be studying Muggle science? It's possible that this was mentioned, and I've forgotten it, or that (since EY probably won't write sequels, the subject will need to be left to fanfiction of HPMOR.

It hasn't been, except for Harry's suggestion in the latest chapter. Most people, though, still haven't been exposed to any noteworthy Muggle science except individual "clever tricks" as used by Harry - nothing to compare with the obvious power of magic.