I'm pretty sure the first exploits for the Wii were done from the gamecube mode.
Nope, Twilight Hack was the first, and it was a modified save game for the Wii version of Twilight Princess. It's actually harder to hack the Wii via the GameCube mode, since it basically locks out access to the extra Wii hardware. WiiU is exactly the same with regards to Wii backwards compatibility (i.e. it locks out WiiU functions when running in Wii mode), so there's no reason to cut backwards compatibility.
Also, this isn't the first Wii exploit known to work on WiiU, SmashStack still works.