Japanese books on iPad
The iBook Store does not have any Japanese book as of now. Apparently, there are issues between the Japanese publishers and Apple.
Better alternative is to use eBookJapan. They've got sizable selection of manga (largest in Japan) as well as literature. You download a free application called ebiReader from iTune Stores, then register and purchase books from the eBookJapan site (
http://www.ebookjapan.jp). Works like the Kindle Store. A manga book is around 300-400 yen (but they come in series!).
If you want to read classic Japanese literature, you can try iBunkoHD (i文庫HD on iTune Store for 800 yen). This app allows you to access the Aozora Bunko, an online library for copyright-free Japanese literature including classics like Akutagawa Ryunosuke and Murasaki Shikibu. While you can access Aozora Bunko free from a browser, this app allows you to have features like page-turning and bookmarking.
Happy reading!