the vsync code is around 5 lines. Believe me, its not that
it may just be the aforementioned lag on the fps counter, or maybe the fact the ATI card takes time to get back up to speed once its stopped.
As for NVidia - i haven't looked too closely at any Doom3 screenshots, but i reckon there is very little difference between the percieved quality of NV and ATI. So basically, NVidia are just being smart and cutting down complexity where its not needed - which is the whole point of high performance programming. I don't see much wrong with that - infact good on them - it probably cuts down texture memory usage too.