Most likely not. If your sysNAND is restored to stock with no traces of GM9/Luma/B9S, you turn in a completely rewritten wiped SD card, and you make no mention of hacking the 3DS, Nintendo shouldn't have any to reason suspect hacking. You should be fine in that case. Good luck with repairs!
Edit : If you're super paranoid, after restoring the pristine stock sysNAND, update to the latest firmware, set the time & date correctly, and add a few free whatever eShop stuff. Log in some play hours if you can. Make it seem like it's been used somewhat. Or don't turn in the micro SD card.