It would count as emulated, but just to be clear. It's not VC running it right? It's some emu you have on the Wii? From what I looked into, those may run slower than console would but I don't know too for sure yet if it should be disallowed. So I'll update with you again as soon as I can.

Actually, after looking into it some more, I've decided that unofficial WADs are not a good idea and will not be acceptable for running. I apologize. If you can emulate in a more official method, that is fine.