I'm pretty sure it wasn't a balance issue since the Citadel class is less than half the length of the Wayfarer, has a much heavier armament, and kept its fighter capacity. And themewise given that VTOL capability is basically standard issue in Star Wars Fightercraft there is no reason I could see that a large transport couldn't support a pair of fighters.
Hmmm, interesting. I don't recall seeing the Citadel as an option for a starting PC ship. Maybe I just missed it...