But is that not the same case as when mhtri came out in the west.. it was Pay to play online in Japan and because of the "lack of popularity" became free to play for the west? It doesn't seem like it has harmed the series in japanese gamers minds because of that...
Uh, they did the exact same shit with MH1 back on the PS2. From what I can tell, it didn't seem to affect the series popularity with subsequent releases.
Anyway, trolling aside, if Capcom were smart they'd not only add online to the Western release, they'd also patch it into the Japanese version and use international servers.
Personally I think they should use just use Nintendo's severs just like they do with all their other 3DS games. That way they can use the system's inbuilt friends list too (though I figure they may need to have a separate hunters list that lets you import hunters from registered system friends as well as the ability to add randoms). The only thing that could be an issue with that would be Nintendo's policy on chatting with randoms but I think Capcom has enough political power to twist Nintendo's arm a bit and get the policy revised.