This HAS been answered. Everything will transfer normally. The transferring process won't recognize the Homebrew Channel and so that will stay on the original vWii. As far as we know (I think) the Wii U on the receiving end won't have any evidence that the original Wii had homebrew on it.This questions was posted before, but not answered, so I make it again. What happens if I run the Wii U Transfer Tool after installing HBC on the vWii? Thanks.
It will overwrite your saved games but your vwii will still be modded.