They won't though. This price break is for the holidays. At this point, they probably can't afford to keep it at $350. This was likely a move just to get more systems in actual people hands to increase software sales especially of exclusive content.There we go, if MS keeps the price distance, the XBone has a good chance of making a good comeback.
More systems = more software sales = more developer support = more systems selling at the $400 price tag
Edit: Also, pretty much every current gen system is bombing in Japan currently because none of them have games the Japanese want to play. The systems all currently have a high western appeal, but clearly the Wii U isn't doing it for them and the PS4 and Xbox One are far more west friendly. The PS4 needs Japanese friendly RPGs and the like to move systems there. They need games developed in Japan that appeal to the Japanese that acknowledge their culture and gaming preferences.
Developing for the 3DS may have been smarter, but at the same time, Disgaea DS only sold about 180k units. They may not have wanted to take the risk of not reaching that number again on a Nintendo handheld. Had Disgaea DS sold better, there would probably be more faith in Nintendo handheld systems. To add to this argument, Disgaea 4, previously a PS3 exclusive and still a Sony exclusive sold 540k on the PS3 alone. All in all, Sony systems show more hope than Nintendo systems. Another fun fact, Disgaea 4 actually sold the most in North America, selling 250k of the 540k units.