Of course it can be done, but would they do it is another question. I know that I wouldn't want them to do it, especially if it's a remake. If it's a port, then maybe, but I would much rather that the port was done for the Wii U rather than for the 3DS.
I'm sure it could be done, but I really don't want to see it happen. The last thing we need is s focus on remakes rather than new games. If MM3D comes through, then adding this would make three remakes on a system that would be better off with a game of its own.
Though, I'm sure it could be ported (and not remade) to the Wii U.
I'm not sure if the 3DS could handle it. If it was put on there, then it would probably not be nearly as good quality. While remakes can be cool, Nintendo needs to be focusing more on new games and less on remakes. Remakes really don't add to a series and certainly aren't a new adventure. Besides....I say it's too early for a Wind Waker Remake.
Here's something that will blow your mind: How about we get a new game? *Collective Gasp*
Sarcasm aside, there really is very little reason to remake Wind Waker. It would simply add to the "3DS is nothing but ports lolol" stereotype and would take precious development time away from new experiences.