I had the same question and the answer is no. I was told the the DS slot is not as fast as the GBA slot and there for will not play GBA games. I don't understand why this is just explanation I got.
If you want to play GBA roms with the m3 ds simply you will need a slot-2 device. I recommend the ez flash 3 in 1. It is like $20 and can be run using Rudolphs ez flash 3 in 1 tool. It will give your ds the ability to play GBA roms, use the nds web browser (because of the expansion RAM), and give you a rumble pack for games like metroid prime hunters.