3DS support is a lot different from securing AAA or even AA console exclusives in this day and age. THey would have to have a userbase like PS4 to and a momentum on that level to secure that kind of thing.
monster hunter is a game that could go multiplatform. in fact, capcom probably has been thinking about it - but if nintendo has this rad new handheld in 2017 and monster hunter 5 can be a launch title and have nintendo's worldwide support in continuing to grow the franchise (as they've done for the last three years), then that means they can even secure a game like that in this climate.
the same is true of other, similar titles like dragon quest, sonic, and yo-kai watch. i think that by and large, japan will view ps4 and nx as one platform like the west views ps4 and xb1 as one platform, but in addition, there will be opportunities for nintendo to still cultivate those kinds of partnerships going forward.