It'll happen, nintendo know it'll sell. Even if Nintendo remade Adventure of Link and released it on the 3ds it'd sell.
It'll be awesome when it does happen though, OoT3D didn't diminish the magic of the N64 version like i thought it would, so MM would be wonderful and a lot of scenes in MM would really lend themselves well to the 3D gimmick (not that i used it for OoT aside from the title screen intro) the moon, the mask transformations, and so many other things =].
That and since i've recently broken my promotional disc on the gamecube so i can't play it anymore i REALLY want them to release it, though i dont mind waiting.