Only a very select few flash cards are even booting on 3DS, IF you can get one booting you are then limited to DS mode only. Because DS mode excludes the ARM7 CPU (what GBA games use) for main program (DS uses it for sound) code, the only way I can think of would be some type of recompilation. Essentially a patcher, converting the *.gba to be a *.gba.nds and relinking the calls so it could run on the ARM9 CPU? This is merely a theory however, and in no way should be taken as solid fact. To date I don't believe its possible.
*Edit* I stand corrected, people say the DSTwo card can and will run them. It is able to do this because it has onboard processing.