I have an old Wii capable of bootmii boot2, so I figured I'd take a NAND backup then bite the bullet and run the WiiU transfer. Here are the results, nice and clear for anybody wondering:
Transfer did not affect custom channels (including HBC)
Transfer did not affect injected VC
Transfer did not affect custom SM theme
Transfer did not affect patched IOS/cIOS/DIOS-MIOS
No custom channels of any kind were transferred (obviously), nor were their associated saves, but neither were they removed from the Wii
Restoring pre-transfer bootmii backup did not re-enable purchased VC downloads (no surprise, that's why you have to be online during the transfer), but VC that was on the NAND for the backup is obviously still there, and it runs fine.
Also, custom channels and injected VC install fine in vWii, you just have to do it manually. I haven't tried manually moving a save file for an injected VC title, but worst case I'm sure SaveGameManager will work.
Transfer did not affect custom channels (including HBC)
Transfer did not affect injected VC
Transfer did not affect custom SM theme
Transfer did not affect patched IOS/cIOS/DIOS-MIOS
No custom channels of any kind were transferred (obviously), nor were their associated saves, but neither were they removed from the Wii
Restoring pre-transfer bootmii backup did not re-enable purchased VC downloads (no surprise, that's why you have to be online during the transfer), but VC that was on the NAND for the backup is obviously still there, and it runs fine.
Also, custom channels and injected VC install fine in vWii, you just have to do it manually. I haven't tried manually moving a save file for an injected VC title, but worst case I'm sure SaveGameManager will work.