Wind Waker HD is a remake. Remake means game itself has been modified and recompiled. It is no longer a GameCube game, but a Wii U game.Well, Wind Waker runs at 1080p, so I would never say never. More than likely, Nintendo will release some gamecube games as downloadable content running at 1080p. There is nothing actually stopping a gamecube emulation engine from internally rendering polygons at 1080p. It is just a question of someone having access to the Wii U-mode hardware (or a hack workaround for vWii) and coding the proper emulation engine.
Considering that there are two "emulators" for the gamecube out for the Wii, it is hardly unreasonable that someday we might see gamecube games rendered at 1080p on the Wii U. I would not hold my breath, but this could help with the vector stretching.
Nintendo already did it with Windwaker and I bet we will see downloadable content that renders internally at 1080p, even if they don't add new textures or features.