If you mean DSi Enhanced/Only ones then that depends on the Flashcard's capability, those who say that they can play them then they can :/
My Acekard for example can play DSi enhanced ones without the enhancement, as the DSi functions are not supported
I have yet to see a problem involving a card that can be opened on the 3DS but fails to load games, Rest of the games should play fine, other problems I have faced are regarding the codes, some codes that required button combos like Sel+UP dont work anymore due to the changes in the button's memory itself or something like that.