Which SNES core are you using? SNES9X 2002 and 2005 both run better on the New 3DS due to being based on earlier builds of SNES9X, whereas the SNES9X (no year) core is based on a more modern code base and therefore runs slower. The tradeoff for that speed is less compatibility, but still good enough to play most games.
Generally speaking, which build version are you using? I'm still using the 1.4.1 builds, and Genesis Plus GX still runs at fullspeed for most games, although Sega CD games will slow down due to Gen Plus GX being a more accurate emulator and having to emulate CD reading and whatnot, basically. If this slowdown has been introduced in the new 1.5.0 versions, then I have no idea, because I'm not using that version. The 1.4.1 builds are still working well enough for my tastes, hence why I haven't updated.