If the ROM runs normally then the hacked version will most likely work- there are no emulator only ROM hacks for GBA games that I am aware of.
Theoretically you could probably make a hack, quite legitimately no less, that troubled the DSTwo's kind of speedpatching but would be fine on regular hardware but I am not aware of anything like that at this point. Were we talking NES or SNES then even leaving aside the emulator only hacks all bets are off.