My logic only applies to how Capcom is dealing with MH. Honestly there was a time when both Vita and 3DS were at the same price tag, 3DS was selling awfully and Capcom still made the jump to the 3DS even getting Nintendo to create an accessory so that people could play MH easier, or in the same way they could have on the Vita.
If you really look at the assets used in MH games from the PS2 era they have pretty much stayed the same, along with the graphics. You have PS2-Wii jump that ensured that, then Portable series on the PSP which maintain the same standard of graphics and now PSP or Wii jumping to 3DS.
Now I don't doubt that Nintendo offered incentives, whereas Sony thought 'we made this awesome handheld that developers actually contributed to creating, it's what they wanted so they're bound to make games for it' and left it at that (it was a half step away from their PS3 attitude and one mistake that they seemed to have remedied with the PS4.
All I'm saying is that even if there is a 3 year deal with Nintendo for MH, I doubt we'll ever see MH coming to Vita simply because staying on the 3DS is making too much sense when it comes to the games' development.