yes, there is a speed difference. not only in frames per second but in sound as well.
yeah, it's true the DS2 can emulate GBA, but it is only what most people call "acceptable." and the SNES emulation seems like even more of a proof of concept than a full, working emulator.
no games currently run at full speed.
disabling sound and forcing frameskip to manual and 1 provides you with a great speedup too, but at the cost of all your sound. and this doesn't work on all ROMs.
it basically goes unsaid that there are huge flaws with the DS2, a couple being that due to the bandwidth limit on the cartridge:ds gate, the CPU harms your FPS on retail DS ROMs.
and the GBA emulator, of which all the fuss is about (lol), is only acceptable to those who have no other means of GBA emulation, or don't mind playing laggy games.
although the DS2 does offer great anti AP, if you have a PSP or some other handheld that can emulate GBA at full speed, stick with that.