A level 54 zapdos found on route 7 in the air and with max lure and 31 pidgey catch combo
According to Serebii, there's a chance to find Zapdos, Articuno and Moltres on multiple routes while in the sky.
After beating the game and catching the Legendary Birds, the Legendary Birds will have a chance of appearing in the Sky as Rare Spawns. They are incredibly rare, with a 1 in 2000 chance so it may be a long wait. Lures increase this by giving you two rolls for each spawn.
Source
After you beat the league they have a very small chance (about 1/2000) to appear on all routes. Hope this helped.