Even if Nair had literally no advantage over fair, it would still have one use: stale moves. Fair is one of Sonic's best gimping moves along with homing attack and spring drop on certain characters, so if your opponent is getting into the kill zone, it's best to save your fairs for the final blow.
Second, Sonic's Fair hitbox doesn't extend across the length of his body, and his bair takes a while to pull off. If you find yourself with an opponent behind you and too close for comfort (and don't have time for a bair), Nair is your best bet.
Third is the combo aspect, which was already mentioned. I would clarify a bit in saying that their landing lag is equal (i.e. non-existent), unless you try to fair close to the ground. In that case, you end up with probably .5 seconds of landing lag.
Finally, Nair is really, REALLY good at killing Pikmin.
In response to Garuda's comment, the fair seems to do a bit more damage coming out of a side/down-b, so it's probably usually a better idea. However, if you're trying to keep the fair off of stale moves, nair is certainly a good idea.