Modded devices can be worth something notable over and above what the baseline Switch goes for. Might be worth swapping them out with someone that wants something, even as a base unit (keep any joycons and dock but just the unit itself), and maybe getting a little something extra on top of that.
General policy is and has always been, probably always will be for any kind of vaguely non crack smoker produced security, if you hack then you lose online, anything you get is a bonus. However if you have the clean backup made before any mods were done and never took it online with them then you could restore that and be as safe as reasonable.
Obviously Nintendo's security is something of an unknown and it is not impossible that if you did not keep it offline that some flags were tripped and just waiting for you to join again/them to need a boost in sales. Likewise if you kept any save games that might be cheated or not readily done by normal play then yeah.