Okay, so I just checked the mod status on both Wii U's, for other users stumbling up this thread:
If you do a system transfer, you have to rehack the vWii modes of the source Wii U, as it is formatted at the end of the process, also trashing the Homebrew channel and other data. The instructions however are exactly the same as for an untouched Wii U.
If you hacked the target Wii U's vWii mode before the transfer, you won't need to do that afterwards, as the data is merged on the target console.