3 possibilities for anything barring the inconsequential it is that bit closer to dying from old age
1) If you use some random hackjob dumping tool then it might use the wrong voltage or bad protocol (had bad reads freeze some carts/devices, never seen it for a game console though and given such things are designed to survive little kids yanking the thing out when running I would not expect to). If you saw something like this in the past for another device then yeah, however here you are using the original device in what is essentially its original purpose so yeah.
2) If you dump the private header (3ds games have unique keys programmed into each that is used to access online, or would have been if Nintendo were not world class incompetents and allowed any key from any game to work for any other game) and share it then yeah, same for any hacked saves you write back but we have not really seen bans in a while now.
3) Above mentioned save fiddling. Flash memory has a write limit. However modern flash memory used in such setups (there is some exotic stuff that costs more than normal but is faster) is pretty robust such that you could probably spend the next several years hammering it 24/7 and probably still then use it as your main game for the rest of your life without any worries beyond general cart ageing.