When you do the official transfer, your regular Wii is wiped clean just like you bought it. You should, however, be able to homebrew it again easily. It will not stop you from using Letterbomb or Smash Stack or whatever exploit you prefer on your old Wii, however all your current homebrew will be deleted. What you could do is take a BootMii NAND backup of your old Wii, do the the transfer, and then restore the backup from an SD card (after re-hacking and installing BootMii) to the old Wii. Let me make this step by step for you:
1). Take a BootMii NAND backup of your Wii and save it to an SD card. Transfer the backup from the card to your PC.
2). Do the official transfer procedure between the Wii U and the Wii.
3). Re-hack the old Wii and install BootMii.
4). Transfer the backup from earlier onto an SD card and restore it to the Wii.
--Results--
Your Wii U has all your shop-purchased games on it.
Your Wii is sot-modded just like it was before the transfer, an exact copy.