Though I am not Japanese, I read a lot of Japanese books. There is Amazon Japan from which I used to buy books. Fortunately, the second-hand Japanese book shop chain Book-Off opened a shop in Paris a few years ago and I can go and browse there.
For reading Japanese on an ebook reader I use a Bookeen Cybook Gen3. I download out-of-copyright free books from the Aozora Bunko site in html, convert them in MobiPocket Creator and read them on the Cybook.
Here is the link to Aozora Bunko:
http://www.aozora.gr.jp/