It's not like there already are easily-available methods of cloning nearly any Pokémon in Gen III, IV and V, right?
If Animal Crossing could have something that constantly checked your save file to see if you changed anything in the SD card and deleted everything if you tampered with your data, a Pokétransfer app could have done the same.
Those generations are not this one, as well, copying data does not modify it in any way. If the data was stored on the SD card you could make copies of it forever and it would be impossible for the 3DS/App to know.