I think the 3DS doesn't emulate GBA, but runs natively. Some temper told me this theory and I found this quiet plausible:
- When you open a gba title the "Nintendo 3DS" logo doesn't appear like in the NES, GB, GBC and GG emulators, but opens directly like the DS/DSi titles (it indicates that it doesn't run in 3DS mode)
- When you are running a GBA title you can't go back to the home menu, just like the DS/DSi titles
- When you are running a GBA title, closing the lid doesn't make the game pause like the DS/DSi titles (indicating a GBA mode)
If that's true, making use of online game or adding new features to gba games may be difficult or even impossible. You can see that they couldn't even add a sleep mode in gba games...
EDIT: Actually in the DS/DSi mode the game need to be coded to stop when the lid is closed and gba games obviously aren't coded to do so, so my third point may have a little flaw, but I find hard to believe gba games run in DS/DSi mode