That's pretty much the only option. The 3DS has no slot-2 so you cannot run GBA natively, emulation is the only option. Of those carts with a GBA emulator, the DSTwo has the best and is the only recommended cart that can do GBA emulation. Same sort of deal with SNES, the DSTwo's the best.
If you're getting a 3DS for emulation, though, I'd recommend something else (like a PSP). "The best" is relative, GBA and SNES emulation is still slightly laggy and imperfect even on the DSTwo (and is worse on lesser carts). The DS is a highly underpowered machine, and while the DSTwo has it's own processor to offset that issue, it's still got limits and isn't enough for the best gameplay.