They should. From what I read, the digital release of Ocarina of Time 3D is just copy-paste from the cartridge. Though depending on what you need done for newer games, you're going to need the latest Boot.3dsx and the latest release of OoTHax, which can be installed via the normal OoTHax installer.
Rumiko Takahashi got so much fan email about the character that she brought her back in the manga, it was going to be completely different originally (with the alien of the week type).