No problem. Try telling them that modding the 3DS only adds a little extra functionality to the console, it doesn't take anything away from the console. Everything a plain 3DS can do is the same after modding it, the difference is that there is some extra coding in there that can be activated as and when you want to use it. It's like putting an extension on a house; you don't need to use it, but it's there for when you want it.
There are lots of benefits involved with CFW that Nintendo will never give to people. Being able to back up saves, copy your games and preserve them, mod them if you want to, play the game without the cartridge (which will help when the shop closes and you can't buy digital-only games anymore).
The CFW you've put on the console ensures that it doesn't decrease in usability and value once Nintendo close the online services.
You've not installed some criminal's illegal code, you've use community-made tools that are safe and professionally made.