But at that point it sort of stops being emulation and kinda turns into a port or a remake. The original game had that slowdown, and this is the original game running on your 3DS, so it has that slowdown. Those kind of things are almost always better left untouched because, like TheMoon said, a lot of people prefer it that way not only for nostalgic reasons (which are important when it comes to Virtual Console) but because they know the game in and out by now with that slowdown accounted for, and that's specially important in action games that lend themselves well for speedruns, score attacks, etc.