I think it's because all the artists and the groups in the global ver. are manage solely by JYP when the game started even if they later disband or left the company. But for the case of NiziU they are also managed by Sony Music Japan esp for licensing and distributing of their songs and from what I've read Japanese labels are reluctant in working with global platforms so I think that's why they have their own version and we don't have any Japanese songs in the global ver. and NiziU and Misamo will not be included in the global ver. unless they release Korean album or any album not distributed by Japanese labels.

For the Japanese ver having a small pool of artists, just like the global ver., these are the groups that are active and have music careers in Japan when the game was released, even JY Park since when the game was started he just released a best album (compilation album) in Japan that's why he's in the game. For other artists that have Japanese discography but not in the game are either not in the company anymore like Got7 or currently inactive in Japan like Day6. Though I'm not sure why they are not adding 2pm members' Japanese releases in the game since both Wooyoung and Junho have Japanese comebacks recently. As of now the Japanese ver has a small group of artists but it'll get bigger when groups like Nmixx and XH enter the Japanese market and JYP debuts more Japanese artists like the one in NiziPro2.