That's literally not what happened here. And again, freeShop is not illegal, it falls under the very same laws that any download manager falls under. Being that freeShop does not use Nintendo's code, does not advocate piracy, does not give keys, does not tell you to use illegal keys, does not provide links to these keys, etc. It does not violate any copyright laws. This the nature of downloaders.
This would basically be like putting someone in jail for having uTorrent installed on their computer, even if they've never used it for piracy.