Linking it up with hacked 3DSes via wifi is plausible, if a hack/homebrew was coded on the 3DS side to accept GBA multiboot/link cable data over wifi. That's as long as the wifi on the 3DS is fast enough, and it would probably require modding AGB_FIRM. If someone modded AGB_FIRM to support that, and then loaded a GBA BIOS from GBA VC, the BIOS should take care of the multiboot. I'm not sure if the wifi would be fast enough though, even linking GBA games locally on a PC or linking Dolphin with a GBA emulator for say, Four Swords Adventures is problematic at best due to how everything needs to be synced up at all times.
I could never get Four Swords linking in VBA-M to work. Four Swords Adventures linking between Dolphin and VBA-M sort of worked, but slowed down the game (probably in order to keep in sync) and randomly disconnected the GBAs or froze.
GBA linkage is just really picky.