Try clearing the cache from Dolphin. Its either a setting, or you can just go to the "Dolphin Emulator" folder in "Documents" and delete the cache folder. You may get some microstutters in games when the cahce is rebuilt, but it may fix your problem.
I don't think that LoZ: SS suffers from a slowdown like Twilight Princess does
I don't think that LoZ: SS suffers from a slowdown like Twilight Princess does