First problem is time. I'm sure you know, games take time to develop. So the later Nintendo knows about the deal, the later they can react, that's why keeping it under wraps until closer to the game release makes sense.
Second, that's absolutely how this deals work. Sony had no idea of the MH/Nintendo deal, they were sure MH was going to be released on the VITA, and that announcement effectively killed the handheld. Sony was sure it was coming, they counted on it, VITA was designed as a MH handheld.
Did Sony know about the TR MS deal before it was announced? Or the Titanfall deal? Did Microsoft know about the SFV deal before the announcement? Did Nintendo know about Soul Calibur 3? The answer to all of those is a resounding NO.
Finally, in bizarro world, were we start from the base that the rumors are true, I would expect Nintendo to contact Capcom after the deal leaked, be more open about what the NX was and try to work another deal, like reviving the MHP brand and have the main team develop it.
But as you see, a substantial part of this deals is that the competition don't know about them, because if they do, they can react.
One thing is certain though, MH will be on Switch.