Did it slow down on the snes like that? I got some serious slowdown playing Mario 2 akin to what you would get on the nes, I guess it's emulating it faithfully.
As others have pointed out, this is a feature (of sorts), the original SNES would slow down when taxed. Seems the emulator is extremely faithful as I have seen slowdown in NES games too. I've never DLed LoZ on Wii VC, but it seems that the slowdown on that game is present in the 3DS version.