I asked a Japanese acquaintance, who works for a shukanshi (weekly tabloid magazine), about Densha Otoko, and he said that there’s a common view that:
Someone at 2-ch (specifically, Nishimura Hiroyuki) and a commercial writer planned out the project, aiming at publication, and intentionally manipulated the 2-ch thread. Nishimura has made anywhere from ¥X,000,000 to ¥X00,000,000 in royalties from the publication and the film/television adaptations. As a manager of 2-ch, Nishimura continues to lose libel/defamation suits for things written on 2-ch and has had to pay several million yen in indemnities, which he is unable to pay. So the idea is that he planned the publication of Densha Otoko as a way to be able to pay off the libel fines.
The reason that debunking the story hasn’t taken off in the shukanshi world is that Shinchosha is the publisher of the Densha Otoko book, and they happen to own the most vicious weekly magazine, Shuukan Shincho.
This is infinitely more interesting than my original conclusion: the runners of 2-ch had to create a media hoax in order to pay off the libel suits born from the anti-establishment rhetoric on their site. And the reason no one is barking about it is because both mainstream and outsider media companies have vested interests in the project’s success.