There's no avoiding from Nintendo learning your n3DSXL has custom firmware.. I suppose since it's out of warranty, they'll repair it back to working condition regardless if it's been hacked. So long as they get paid, the worst I foresee is that Nintendo uninstalls the CFW. You would be left with rehacking it again with Seed/Steel/Frog/Fredminer, or NTRboot if you have a DS flashcart. This is of course assumes that motherboard is intact, and they don't perform Format System Memory or reflash the NAND where you lose the original movable.sed tied to your Nintendo 3DS folder.
As far as your parents goes in finding out, only you would know best how they would react if they learned your handheld has CFW. If they're strict and uptight about that sort of thing where they'll severely punish or ban you from video games, I wouldn't mention it. I don't know what your morals are about lying to your parents to get them to repair your 3DS. I know from my younger days, shitty me would have stated that 3DS was accidentally dropped instead of how it was smacked out of rage. If you do lie to your mother & father and have any inkling of good within you, just know your gamer soul will no longer enjoy playing video games when the guilt gets to you for stealing from your parents to fix your mistake.
Without knowing anything more than typical parenting, I would avoid revealing the CFW but be truthful about how the n3DSXL broke due to negligence. You're going to have to somehow relate to your parents about rage quitting in ways they're familiar with.