These Kindles are actually cheaper than those in the US (normal version is around the equivalent of $105 US) and I don't see any mention of advertisements on the Kindle itself.
Not sure about prices. I just checked out Anthony Everitt's The Rise of Rome on Amazon and it costs me 2,091 yen. I can get it on the Kobo book store for 1,498 yen and if I use one of the coupons that brings it down to around 950 yen. I don't know about other books but if that's what the prices are like then I definitely wont be buying from the Kindle bookstore.