If you are talking about the Sega 3D Classics on 3DS, you are simply wrong. These are not emulated and were remade to add 3D. There is no emulation taking place at all. They are also not laggy in the least, nor do they have sound problems. But then I use a New 3DS XL which is not only faster, but has the best sound quality of any 3DS/2DS system.
I agree there is no lag in those titles on the 3DS, but I remember reading an interview with the M2 guys and they said they pretty much made a custom genesis emulator for the 3DS that plays the games like a genesis game without issue, but also outputs in 3D which requires customizing the rom for proper output. So I believe it is in a sense emulation, but it's not just simply throwing an old rom on the 3DS either. This virtual Sega 3D system that gets emulated became known as the Sega Gigadrive.