are you talking about for a DS flashcart?
if you are asking about a gateway or sky3ds. the gateway requires files on the internal sd card... and the sky3ds i am not sure if you will need to use a special format to it..
if its a DS flashcart then yes you can use it but it is not really recommended, use it as a temporary solution til you get a real card. they are cheap...
why its not reccomended to use? because the flashcarts are usually cheap made and can easily break something like the spring, and since its hard to remove only the sd card from the flashcart, its a tedius process.. each time you want to remove the sd card you will remove the flashcart too, til the plastic wears out and breaks...
personally, just copying files to the micro sd on my DSTWO is a pain, i hate the trouble of ejecting the dstwo, take out the sd card, put it on the pc, then insert both cards again on the ds... sometimes i just use the stylus to remove the card from the ds but it is still not really praticall