I think the limits of aircraft was just because with collateral damage considered, they are just way too powerful. A stack of a 100 good units comes at you, and you pound it with 20 bombers, and the units you use to mop up won't even get any experience points.
but they have no limits on the number of artillary you can in a single city either. just seems strange they limit the number of aircraft but not any of the land or navel units.