I'd say the domain for the site that hosted the title keys actually was DMCA'd by Nintendo, and the domain host removed the IP address from it's listing. So now all ISPs that get all the DNS packets would just receive the packets as "up-for-sale" domain being stored in their DNS servers. Not in any way related to freeShop, but I thought that this would be the exact reason why it happened, I know it did happen to a certain ROM site about a year ago and they had to switch domain providers.
That's why everyone's getting the "sponsored listings" instead of the site. So yeah, all that remains now is just the site's IP address, which can only be accessed by typing in its IP address.
But if anything, I'm sure freeShop could live on as some other project that doesn't connect to the CDN servers.