Ok, let's look at it from this angle:
Let's say just like nose art, each aircraft is set up to display the number in a specific position (IE, in F4Us it's on the front landing gear door and on each side of the fuselage forward of the roundel). The problem is, skins in the game already HAVE aircraft ID numbers as part of the skin. HTC would have to toss out the skins and institute generic, numberless skins otherwise your individual plane number will get lost against the number already part of the skin. Additionally, each skin would need to be very specifically designed to ensure the number wouldn't interfere with any other artwork (odd-sized/placed national insignia, etc).
I like the IDEA, as it would offer both immersion, and would look really sweet in screens--especially integrated with the ability for squads to create their own unique skins rather than just a nose art file--but I don't see this working with the way skins are currently handled.