You don't need to worry about compromising the structural integrity of the bus by cutting a hole in the sheet metal of the roof, as long as you're not cutting through one of the ribs (which are usually called hat channels here because hat channel is the type of beam shape used for them), and even then you could cut through one or two ribs without much concern. You do have to worry about any new opening in the roof leaking, but that's par for the course.
Lexan will bend over this curve (it would probably need the assistance of heat) and can be screwed or riveted in place, along with seam sealer to keep it leakproof. 1/4" would be strong enough even if it were totally flat, and the curvature will strengthen it substantially anyway (by "strong enough" I just mean enough not to break - it does not need to do the job of the steel sheet it is replacing).
FWIW they do make ventilation fans that are sort of translucent or transparent, so you can get a sort of skylight and also a fan at the same time, and just as easy to install.