1. Mages do not have Ride as a class skill. You will have to send warrior-mages up in the air who can cast invisibility and have the ability to stay in the saddle. However, this brings us to
2. See Invisibility allows you to see invisible things in your sight range... but neither fighters nor wizards have Spot as a class skill. A Ranger/Wizard would have a few ranks in spot, but the distance penalties mean that the 3 levels of Wizard it took to get See Invisibility reduce the chances of making the spot check for a very distant target.
Of course, it could be argued (and I would probably support it) that you don't need to make a spot check to see something very obviously there, like a person flying in the air*, so maybe this isn't that big of an issue.
*Which, incidentally, now raises the question of camouflage...
You're making things too difficult. If you're doing siege warfare which features stuff D&D wasn't designed for, you need new items and rules. Otherwise the whole thing just isn't gonna play well anyway.
So you have your griffin rider prestige class which is designed to locate and engage flying enemies. Or you have your goggles of flying invisible spotting. Or what have you.
There's an answer to every objection, and it lies in the area of "the game would need a sourcebook covering such engagements". Absenting that, shoehorning D&D combat rules into a mass engagement structure is gonna require some work.
For me, it means let your imagination run wild then work out how to do it. Magic items, artefacts, new spells and classes - all this would be needed to run a satisfying battle if that nature.