Thats a valid question, that has been batted around a bit but never explained.
On one hand the GC controller has all the buttons needed except select (which could easily be mapped to the Z button) on the other hand the VC controller is an attachment for the wiimote so the GC signal is potentially going in the wrong port.
It is fairly well known that SSBB is intended to be played using the GC ports so I don't see why VC can't be configured to also accept input from those ports if a Wii game can.
I don't have an answer, and it may be something that isn't known until you get a Wii and attempt to use the GC controller with the VC. Those are just my thoughts on the subject.