The second it was known that a long-forgotten 3DS game called Cubic Ninja was the key to unlocking homebrew on the device, gamers began tripping over themselves to find any and all available copies. This has quickly led to a sharp inrease in its aftermarket price tag as word continues to spread. Naturally, the word has reached Nintendo's ears, and the company is doing what it can to avoid any damage that homebrew could potentially inflict.
Tiny Cartridge has reported that Cubic Ninja has been pulled from Japan's eShop, effectively killing the game outright since it was only ever released digitally there (and preventing homebrew from being installed on Japanese 3DSes unless another exploit is discovered). We don't have that problem out West, since it's only available in physical form here.
There's very little worry that the exploit will be patched out, since the game's developer, AQ Interactive, was absorbed into Marvelous and technically no longer exists. The way the exploit works, there's nothing Nintendo can do to plug it up short of pulling all copies of Cubic Ninja from retailers. That doesn't sound likely, but that doesn't mean Nintendo won't attempt to find some other means.