I actually got around to some tests. Gambatte .cia is running fullspeed on O3DS after all, which is great. The only game I tried that doesn't run fullspeed all the time is of course Shantae, but it's pretty close, it just dips to 55fps sometimes. It also doesn't have the audio crackling that ruins gameyob for me! Hurray for accurate GB/C emulation on 3DS!
Also, somebody mentioned FCEUmm was running fullspeed on O3DS a few pages back, but that's not the case for me. Dunno why, only getting about 40fps. It's .cia instead of .3dsx, does that have any importance?