Not sure if it was discussed before, but
@cearp's post gave me an idea (no, it isn't about a backdoor).
What about giving this utility two modes, a locked mode and an unlocked mode?
Basically, the locked mode asks you for the pin to boot, then it goes into unlocked mode. In unlocked mode, you can turn your 3DS on and off without any pin input (useful if you were doing a lot of stuff with H9, D9, whatever and don't want to be bothered with your pin, or if you are at home and know you are safe). And using a key combo (that doesn't need to be secret) at boot, you can choose to put it back to locked mode.
For example, (and that's where
@cearp's post comes in), the 3DS knows it's "unlocked" when a certain file is present on the SD, and to go back to locked mode, the utility just has to delete this file (and if the SD isn't present, the 3DS is automatically in locked mode).
But this is not a backdoor because this file here would have to contain a hash of the password or something, this way, an external user can't easily just put a file on the SD to unlock the console.
And btw, this also solves the "what if I forget my password" problems, one would just have to go in unlocked mode (at a time you remember your pin) and save your "unlocked" file on your PC. A stealer doesn't have that file so you're still safe.