Actually, there are plenty of current Japanese ebooks available (and a lot of e-manga), but they mostly use formats which are currently not convertible. Two most prominent right now seem dotBook and XMDF. Here's a few links to shops.
インプレスジャパン ダイレクト
http://direct.ips.co.jp/book/impressjapan.cfm
ウェブの書斎
http://www.shosai.ne.jp/
電子書店パピレス
http://www.papy.co.jp/
BitwayBooks
http://books.bitway.ne.jp/
PDAbook
http://pdabook.jp/pdabook/
楽天ダウンロード
http://dl.rakuten.co.jp/book/
SpaceTownブックス
http://books.spacetown.ne.jp/sst/
And of course, the Japanese counterpart to Project Gutenberg is Aozora Bunko:
http://www.aozora.gr.jp/