That terminology "fake FPS" have always make me wonder
How I understand it, one could say fake lecture of FPS, but is not what is being meant. I believe is meant "despite the FPS is indeed that reported, the actual image is being sampled in wrong timing", as to say it is not "moving as it should" but the number of frames being sampled per second is correct.
Contrary of movies (in celluloid) where the image and the frame are inseparable, in PC environment the image and the frame aren't so rigidly tied. This is still valid even in emulating console games where ideally the image and the frame should be that inseparable as well.
PS: Since much of the internal sync in the emulator is done based on the frames (and not the image)... that "lag" introduced by some the speedhacks and dependent on the games, might still be preferable than raw low FPS... but each case is a case and generalization does not help here.
Contrary to the popular belief, EE Cyclerate is more prone to cause desync than VU cycle stealing (and is the main cause of subtitles and voices desync). The most common collateral effect of VU cycle stealing is the above mentioned "lag". But, repeating, that depend a lot on the game being played.