I might be mixing in how Nintendo 64 emulators do it vs snes. Makes sense since the N64 has actual models and stuff. Textures and all that. Although snes9x has some very good filters that remove almost all pixelation without ruining the look of the game even on a huge screen.
Oh yeah, 3d Models upscale much more easily; leaving you with the texture files to be rescaled or modded out.