I seriously doubt that any 2D Zelda games will be released in full-3D card format. What I see happening is 3D Classics versions of the first three games (NES and SNES are the platforms designated for the 3D Classic series). Those aren't direct ports, though. The existing 3D Classics were rebuilt from scratch, using the same sprites but on a higher resolution screen with the 3D effect built in. For A Link to the Past I expect basically the same game but with a wider viewing angle and slightly reconfigured HUD icons to fit the resolution. Then they throw in the alterations to the graphics that take advantage of the 3D effect when turned on.
I have to wonder how much it will take after the GBA version. I'm inclined it will include most of the additions and the retranslation (Excitebite and Xevious weren't exclusive to the NES, so I would hazard a guess that there were some slight alterations to the NES version and that the 3D Classics were made as faithful to the prefferable version as possible). I don't know how they'd deal with Four Swords-related additions, though. Theoretically the save data could interact with the DSiWare game's save data, but I find this somewhat unlikely considering the separation between the two platforms, although both games could easily be kept on your 3DS. In the very least, I hope that of the Four Swords-based additions, they keep the Palace of the Four Sword. Some of my timeline theorizing depends upon it, and I would hate to see that damaged by any possibility that it's been debunked as part of the story.