I've had no speed issues whatsoever with Neo Geo games via RetroArch on a New 3DS. I mean ... OK ... the games have slowdown, but that's Neo Geo for you ... there is an option to overclock the Neo Geo's CPU, but even on New 3DS you'll be pushing it. It goes up to 200% speed, but you can really only bump it to like 110-120% without ending up having the reverse effect because the 3DS can't keep up. That does indicate that the New 3DS is sort of cutting it pretty fine, performance-wise, so it's possible you might encounter some emulator slowdown in some games, all I can say is that I haven't seen any that wasn't caused by upclocking the Neo Geo.