I think the bigger problem than damage to the brain, would be damage to the inner ear. The books state that Yeerks have to move stuff around in there, and then basically eat their way through the skull to get to the brain. In fact I've always wondered if Controllers end up with hearing loss in one ear.
Of course, most autopsies don't go anywhere near that area, as far as I know. Heck, do most autopsies even look at the brain? I suppose it really depends on how the person died. If a guy dies of a gunshot wound to the chest, I tend to think they aren't going to open up his skull. Brain cancer, though, and they probably would. Then again, in that scenario, anything that's wrong with the brain might then be attributed to the cancer instead. Hmm. That's an interesting little catch-22. If they think they have reason to look at the brain in an autopsy, then there was probably already something wrong with the brain in the first place, and any damage or irregularities would be attributed to whatever that was, instead of to a Yeerk. Same with the inner ear thing. Convenient.