Not necessarily. Motion controls could be a TV-only option. I'd rather it be there than not.
They could do that, yes. But I don't see them going that route. On the TV you play with motion plus, then you turn off the TV and pick up the gamepad and play the exact same game with a completely different control scheme? It just seems like something that, although possible, would be counterintuitive and they wouldn't bother with.
But at the same time, if the options are there and people can do just whatever they want (Motion/No motion, on Gamepad/off Gamepad), then bring it on.
EDIT: Although one thing that I definitely want them to do is to give me the option to use the gamepad's motion to fine tune my aiming, like in OoT 3D. The aiming in Zelda was never accurate until TP, and Gamepad aiming works well and quickly. So give me that option and I'll be happy.