A lot of the reason why so many Japanese companies skipped the HD generation is because the HD consoles failed to sell very well in Japan. The PS3 crawls along at a steady pace, while the 360, despite being a bigger Japanese success than the old Xbox, is all but dead. I guarantee you that if the PS3 had been as big of a hit in Japan as the PS1 and PS2 that Japanese companies would have been out in force in the HD generation.
That said, some Japanese companies did well in the HD generation. In particular, Namco has been very active this generation and, thanks to some strategic acquisitions, has grown into one of the world's largest game publishers. They did four console Tales games and a number of other HD RPGs, and published outside works like Ni no Kuni and Dark Souls. And From Software has risen from obscurity to stardom on the backs of the Souls games.