It sounds like you're just imagining flyers on another 2-dimensional plane above the one on the ground, which is not realistic. If they can fly, they can be just as far from another flyer as they can be from a guy on the ground. They're not just standing on the roof, they can be above and below each other as well.
If they don't want to be close to a guy on the ground, why would they want to be close to a guy in the air? Either they're wanting to be distant, or not.
Regardless, the mechanical rules are quite clear that flyers can shoot each other with ranged attacks. If you don't like the thematic justification that I use, you are free to invent your own, but that is the way it works.
Edit: The hinderance statement is a good point though. I'm not completely certain how to justify two creatures being far enough to shoot each other yet still creating hinderance for one another.
Well they could if the shot was range 0-2 instead of 1-2. Just as you can shoot a gun even if it's touching your target, but you can't really do that so easily with a bow and arrow. At least I don't think you can.
So there's no conflict between using a range 0 ranged attack and being able to hinder. For the bigger minimum range take a few steps back, or in this case, flap your wings a couple times. For hindering, don't step back and don't flap your wings.
Kind of like how they have to swoop down to make a melee attack against a non-flyer.