The reason you get an error when trying to delete a PNID on your 3DS is the console tries to contact the eShop during the deletion, presumably to unlink purchases. However, Pretendo does not run eShop servers for legal reasons.
Of course I have 0 idea of how in the hell 3DS networking works, but I don’t think it would be much work to just set up a dummy server that accepts whatever packets the 3DS sends to the eShop and returns the confirmation packets.
I remember @PN_Jon mentioning something about this at some point, although I can’t find it right now (Discord search sucks). I believe he said that the console expects a real response from this API endpoint, so a dummy “200 OK” response wouldn’t work. It also permanently stores some of the data in the response, and responding with random junk data might result in the console being unable to access the regular Nintendo eShop again.
Edit: I believe this is the relevant quote from Discord.