Attitudes in Japan are slowly changing.
Most of this is thanks to the Emperor surviving the Tsumani in 2062, then to his "Divinity" with the Kami....
Yomi Island has been officially shut down, but interestingly enough, a large population of Metas refuse to leave, and have been whispering of Seperation from Japan..... (all this can be found in Year of the Comet)
That is not to say that is swell for being a Meta in Japan. Chances are you will still be turned away from just about every business, but they will do it with a smile now.