Yeah, remastered is a good word for what OoT3D is and MM3D will be. didnt think of it, but yeah, thats exactly what it isI have a very hard time believing the 3DS version is going to run the N64 code written for the original game. I think calling it a remake is fair, but it's really a remaster. Same core experience, but updated for a newer generation console with enhanced graphics (and 3D support) and possibly remastered soundtrack as well.
as for the code:
obviously, I can only speculate, but I expect that everything except the graphics engine got ported directly from the original n64 code, including physics and game mechanics with only minor modifications to it. How did I arrive at that conclusion? Well, the bugs that are present in OoT3D behave (nearly) identical to their N64 counter part. Even those bugs that got fixed in their previous incarnation (e.g. Swordless Link, Infinite Sword Glitch), are still possible with slightly different exploits and result in a identical behavior.