What about people who already bought it? Does it stay installed on their consoles? And if they uninstall it, can they download it again?
It's probably moot because I'd expect Nintendo to demand a patched version of the game with Ruby removed to replace the existing version for those who bought it even if Nintendo decides not to allow it up on the store again.
I can't remember them pulling games off consoles - when people discovered games allowing code execution on the 3DS, Nintendo either marked patches as mandatory as soon as they were ready (so you couldn't play without updating) or attempted to block the exploit on the OS side (as they did with Cubic Ninja, since the studio behind it shuttered)
It's probably moot because I'd expect Nintendo to demand a patched version of the game with Ruby removed to replace the existing version for those who bought it even if Nintendo decides not to allow it up on the store again.