I'm not sure, either. With Monster Hunter it could be as simple as Nintendo offering assistance with promoting the franchise and Capcom being annoyed by SCEA blocking Monster Hunter Freedom 3 HD. But it seems like there could be something larger. Capcom was all in on the PS1 and then pulled back a bit the following generation, giving the Gamecube and Xbox a lot more support than they warranted (not coincidentally, this is when Capcom actually did get into financial trouble). The Capcom Five was a very strange move, especially Resident Evil 4 which should have been a huge hit but flopped on the 'cube and forced the company to liquidate a bunch of assets. Either there's a little bad blood between them and Sony, or Capcom just makes really terrible business decisions for no apparent reason.
Is Japan so a lot more casual input into business ideas, deals haapen because friends from different companies have a drink and come out with crazy ideas, then champion it with the bosses. Is apparently how Street Fighter x Tekken and eventually TxSF come about, Ono and Harada are friends and came up with the idea one night. Similar story for Snake in SSBB.
I think game producers in Japan have way too much freedom and voice in the busines side of things, the entire GC mess was mainly Mikami, the decision of where Resident Evil went was up to him and he argued other games for GC too. Is entirely possible whoever does Monster Hunter said he wanted to do it on 3DS and Capcom said 'fine'.
As to MH3P HD being blocked, both Sony and Capcom were to blame, SCEA would not update ad-hoc for whatever reason, but Capcom didn't want to make the effort to meet PS3 requirements in the west like trophy support and some other things. Capcom didn't have to use ad-hoc either, could have gone with normal PSN system. Being cheap.