I guess not really. These games usually implement a metodology named Z-buffering and in theory this should allow generating per-z-index stereoscopic offsetting.
The problem is each game may have it's own implementation of managing the Z-buffer and makes this process slow and expensive in time and resources. For a pc this may be trivial, but for a 3ds probably not.
Yes it's possible. There are homebrew 3D games and there are nes homebrew emulators. All we need it's someone build some kind of converter to convert the layers in nes games to 3D. Like Super Mario Bros has at least 2 layers, the Mario and the scenario. In 3D Mario and the enemies could be "in front" and the scenario back.
Isnt .cia files illegal? I know we dont host them or link to them but we talk about them,.... so if said 3ds 3d nes emulator was not linked or hosted but talked about whats the harm? And if its a anon pastebin, and ninty has it taken down, its just reuped somewere else so who gets sued? Who gets hurt? A anon thatsa untraceable releasing noncommercial freeware?
Heuristic means (from wikipedia): Any approach to problem solving, learning, or discovery that employs a practical method not guaranteed to be optimal or perfect, but sufficient for the immediate goals.
In more human words: it's a set of rules for locating the Z-buffer management and understand it. This searches trough the code of the game for patterns, indexes and snippets of code to locate where the Z-position memory offsets are, and then offer a video reconstruction of the depth.
That, my people, is not trivial like at all. And definetly not possible even for a N3DS at least with raw power. Optimizations may apply, but it's really hard to accomplish at a playable rate.