Series should have went multiplat but I guess Capcom got a few good deals when it was exclusive with Sony originally on PSP and Nintendo with 3DS/Wii/WiiU.
I don't think, initially, there was any deal during the switch to the Wii. It was more that Sony kicked the dog for MH with the 3rdHD debacle. You don't need contractual incentives to just tell a company to fuck off and go to their competitor who also promises to actually give your franchise support in the West and globally.
The Wii port was moderately successful but when the series hit the 3DS and rose to PSP-like successes while the Vita came out with a wet thud and the PSP faded away, that is potentially/probably when deals were actually struck. The co-marketing and localization initiatives (and cross promotional DLC in different entities) that Nintendo then took on with 4U and G, are what I'd think indicate that some sort of contractual partnership was formed and penned by Iwata in his time.
Will that end? At some point, no doubt, though I'd imagine that Nintendo would make future deals very, very attractive for the struggling Capcom to turn down.
Does it matter? Is there much of an audience for these games anywhere but on handhelds at this point? Is it financially tennable or will the RoI be justifiable? Who knows. The fact that they dumped this on the platform, makes me think not at current. This is their token support for everything but the 3DS.