I didn't say had, I said they would be fools not to.
I'm well aware that such a contract would be unprecedented. And if there was a contract in place for Colonial Marines, they probably took one look at that and said "Nah, we're good" back when the third party situation was "typical Nintendo" instead of "historically awful".
This isn't the co-marketing money the big 6 western publishers (Activision, Ubi, Take 2, Warner, EA and Bethesda in order of market share) have relied on for more than a generation. At this point, Nintendo may wish the addicts weaned themselves off, but they clearly haven't. So they're going to have to pay up and demand a hard time limit.
tl;dr: If/when Watch Dogs comes out, Nintendo will have paid for it. Big time.