In the real world you would not put things like radio towers and skyscrapers in the path of airport runways for safety reasons does those things even matter in Sim City 4? Even if the airport is for eye candy?
There's absolutely no game mechanic that would prevent you from doing so or punish this architectural layout.
But like all sandbox games, you could reach a point, where it starts actually bothering yourself. If you've reached that point: congratulations SC4 got you!
I thought so just wanted to make sure. Sometimes playing a game like Simcity it is hard to not use real world thinking when laying out a city.