Cubic ninja was only avaliabe on japan e-shop (AFAIK) it was taken down. If you have a Japan e-shop version then yes you can. Please read the information o the ninjhax site.
WHen it is cubic ninja on 9.2 U/E/J or below it will work
I understood it in the way of you wanting to use the 3ds as a controller. SO this might be what you are looking for https://gbatemp.net/threads/3ds-controller.375443/ ?
Wouldn't it be hilarious if they would message you and say "Please apply a private header to your cia because otherwise we will ban you for pirating/cheating"
Well a anti-counterfeiting measure that you can circumvent isn't really anti-counterfeiting... (that statement isn't legally valid of course)
Well hacking is a technically crime in Germany (and i am pretty sure in America too). And there are still official hacking conferences in both countrys...