I'm familiar with the Japanese e-book stores Kobo, honto.jp, and Kindle, but all of their books seem to have DRM, and none of them allow you to read books on your computer. Are there any bookstores that sell DRM-free e-books in Japanese?
You can remove the DRM from Kindle books and convert to most major formats without too much trouble using Calibre or other software. I am not a lawyer, but in the US at least, you have the right to do so (cf. decrypting DVDs).