1st hit nair can be used for a grab setup, or for a gentleman. Second hit is used for, as you said, combos.
The big difference is the timing, as with 1st hit nair you have to fastfall it, and by doing that you effectively cut off about a third of the time the hitbox is out. During neutral, a healthy mix of both is good, as if you only do single hit nair into grab they'll start just hitting you out of it, or dash dancing, but if you only do double hit then they'll just shield.
Without good nair usage you tell Falco that he can dash dance all up in your space without any punish. Your nair is the equivalent of Falco's laser; good for zone control, and great for setups.
TL;DR: use double hit in neutral a lot if you need some breathing room/are turtling, and you use single hit to set up for a quick grab.