It would affect architecture a bit (lead sheets everywhere in the masonry!), but not much. You'd have more roofed parts within the castle itself (no crenelations in the open air), and you would have arrow slits (obturable in case of rain) in said roofs to allow defenders to fire at flying threats.
The basic principle of walling yourself up and keeping only tiny holes to rain fire and destruction on the enemy stays sound. (Cover bonus to AC and Ref saves! Just what you need against fireballs and dragon breath. And with 3e's initial 9/10th cover, they're even better.)
Even if flying foes are common, the simple fact of forcing them to fly high (to bypass the walls) and being on a high ground yourself is useful.
Now, the real killer are burrowing monsters, like thoqquas, xorns, earth elementals... But most of the time they'll be summoned. A few abjurers can banish them.
One thing I would expect to see in castles is magic circles akin to those in the Miniature Skirmish game. Give +1 attack bonus to those who are on it, and their attacks are considered magical for purpose of overcoming damage reduction. Put one atop a tower, and a squad of archer, and there go your flying, protected from arrows, mage, or your not-that-old dragon.