The 32GG 3GS may be number 1, but the article doesn't mention what sort of market share it takes to claim that spot. I was just in Japan for most of this summer, and I went looking at phones with some Japanese friends. There are just SO many feature-rich phone choices out there from all of the major carriers that no single model really seemed to stand out as a market leader. If the 32GB 3GS got even a small bump in sales, that could have pushed it into first place.
As for the swipe payment option, I expected to see things like Mobile Suica used by lots of people, but it really doesn't seem to be too common yet. Most people still seemed to pay for train and subway trips with regular Suica (or Pasmo, Icoca, etc.) cards in their wallets. It's certainly a cool feature, but it apparently hadn't been adopted by a large part of the population yet.