It's possible they submitted something way over the top instead of what they really wanted to get the censors to object. Then, they submit the relatively tamer, original, version and get it approved. It's something South Park does all the time, so I wouldn't be surprised if anything cut from the American release was actually intended to be in it.
I like how the article neglects to mention that Nintendo is only claiming the revenue from more recent games such as ones on the 3DS or Wii U.
Also, it's not like Nintendo is the first to do it. Sony, EA, Square-Enix, Microsoft, SEGA, Konami, Namco, and a handful of others have done it, too.