AF is the same with both D90 and D5000 meaning same AF sensor. What the D5000 lacks versus the D90 is the ability to power focus on older (non AF-S) lenses. If you stick to new lenses (with AF-S) then you'll have no problems as all new lenses are AF-S.
The way the D90 is able to power nonAF-S (no af motor in the lens) is with the use of a little "screw driver" like protrusion that sticks out of the camera and actually spins and drives the lens autofocus gears. The D5000 doesn't have this ability. So if you buy an old used nonAF-S it will not autofocus on the D5000.
Niko is more understandable then I am so please disregard my post.