Kid Icarus: Uprising is a stylus controlled 3DS game. Unless you are press down as hard as you possibly can while using the stylus, your 3DS should be fine! Nintendo builds its products to be tough; it builds them to last.
Some players, however, get way into their stylus play. Check out this screen guard from one Kid Icarus: Uprising player. Not sure whether it was a stylus or a fingernail was used while playing...