Faster apertures definately makes a difference in Autofocus. 1) They see better in low light, and that helps the sensors, and 2) they have shallower depths of field, and that makes the sensors more sensitive.
Nikon, alas, doesn't make any AF-S high speed primes. However, I have no problems with the D2x and the f2.8 zooms focusing in very low light.
David Buzzard's Technical Blog