Well, there are a number of reasons... First off, there are some companies who just don't do well on mobile and companies who just want to diversify their support. Even in the mobile market, there are winners and there are losers. Companies that see some success in consoles and handhelds will continue to support them even if that success comes mostly from outside Japan and even if mobile is so much more successful.
In addition, it is hard to ignore the PS4's international success. I mean, it has been out for about a year and a half and it is already up to 2/5s of the 3DS's sales which has been out for five years and Vita's sales don't add much more to that. Look at the worldwide sales of both compared to the Japanese sales of both. Nintendo handhelds actually appear to have a future, even if it is a future catering to a specific niche, while Vita is practically a regional system for Japan. Again look at the sales... In just Japan, the PS4 has 3/8 of Vita's sales and is currently selling around the same level the Vita currently is. Gaming in Japan has basically three options for the future: Go mobile and pretty much compete with every other Japanese publisher and developer as well as publishers and developers from around the world in a blue ocean that's quickly turning red, support Nintendo's handhelds and hope that Nintendo's niche holds or gets better, or support PlayStation consoles and hope the international market buys the games. This likely also explains why PS4 is seeing all these PS3 and Vita ports from Japanese developers. Both the PS3 and Vita are living on borrowed time, both are dead outside of Japan, and Vita will not have a successor. Thus, we are pretty much the entirety of what's left of the Japanese developers on PlayStation systems trying to push Japanese gamers onto the PS4 while depending on sales from the international market because their options otherwise are literally to support Nintendo's niche or to go mobile.