Well, currently you find emulators work better on the 3DS for now. But that will change as the development on Switch goes on. Might be a year, might be less, could be more, but the Switch will end up ruling as the portable emulating machine.
While I would have no objection to seeing the Switch become a good platform for emulation (it has iffy controls but workable enough I guess) from where I sit the same things that saw the 3ds significantly underperform are also at play in the Switch, and I am not entirely convinced that it has the resources to rise above.
Or if you prefer the GBA and DS represented some of the best hardware for their times, times in which open hardware was not really a thing. This attracted some top tier talent. When better actually open hardware released, and became popular no less, said talent all but vanished and did not return.
Eh when RetroNX isn't crashing it is already pretty much at the same level as on 3DS for popular consoles. Half the time its the exact same cores running on the same ARM architecture so its not that different, except you can run GBA and PSX emulation at fullspeed, as well as the more accurate SNES/Gens cores. The real advantage of 3DS is probably more Virtual Console, which covers few systems and not always the best compatability, but are highly accurate with what they do play.
There's also an enormous difference in screen quality. Even though you'd think the 240p 3DS screen is enough, you can't play most home consoles in their proper aspect ratio without blurring everything, not to mention the few games using higher-res modes like Secret of Mana. The TN verison of the screens also struggle with motion blur and slow-scrolling black dithering, to the point of making some titles developed for CRTs pretty difficult to play. Conversely of course 3DS is a lot more convenient to carry around and that beautiful 720p IPS is going to make the hard edges of the OG resolution all too clear.
As far as pre-32 bit goes I'd say the software is close enough that I would focus more on which overall hardware you prefer, because they are very different form factors and switch has quite a few ways to play it. In the future if homebrew gets access to 3D, emulating the first gen of 3D is very possible on Switch while that isn't ever happening on 3DS, so if that is important to you it's pretty obvious.