Coming from a rookie who specializes in Java, so I could be wrong. However:
It seems to me what you're asking would involve modification of the emulator that runs in VC to access the 3DS wireless communications and/or modification of the individual ROM for wireless capability.
The former is probably easier than the latter, but I feel the latter will be necessary regardless as the data sent and received must be compatible with the wireless channel it would travel through.
Again could be wrong. But it sounds like more effort than it's worth just to play some Pokemon or Battle Network with your friends.