Yeah, I used to work in the Shinjuku Center Building before they homeless-proofed it. I'm of the stripe that says, provide the means for food, shelter and medical assistance to the chronically homeless and let them decide to take it or not, and ten to be against 'cleaning them up'--but frankly, that tunnel was getting way out of hand. That tunnel is an accessway that a lot of people use to get from the station to work. It stank to high heaven, and you would witness some rather disturbing stuff that I'd rather not get into.

I was not too happy about the idea of moving these people--where did they go? Do they have an acceptable place to reside now? But the whole do-as-you-will thing has limits, when it infringes on so many other people in such a startling way. So long as a reasonable alternative is offered, I think it was the right thing to do.

And yeah, the lipstick garden does look a bit odd...

Luis-
My wife was telling me this same story about the tunnel's previous incarnation as we passed through it, and I agree with you that at a certain point, something needed to be done. But, I tend to view these "maybe people won't realize the real purpose of them" city improvements with disdain. (In fairness, I really don't know what the purpose of these lipsticks was, I'm just surmising. It was also likely that in addition to preventing homeless from setting up camp, they wanted to prevent vendors from setting up shop as well).

At any rate, American cities are full of them. Mike Davis wrote about this in his City of Quartz book.

As for the homeless, I don't know where they've gone, but the large amount of blue in Shinjuku Chuo Koen is hard to miss.

The homeless are still everywhere in Tokyo. You don't see the quasi-permanent plywood and blue tarp houses or tents in Shinjuku anymore, but they are there in the parks and around the station. In Ikebukuro they are much more visible in both the East and West park, also they sleep in the evenings in the underground.
I think they've overdone it with the anti-homeless fixtures around Tokyo. Even near where I live fences have been placed under bridges to prevent homess from living there.

There is a group of homeless and volunteers that patrol the Ikebukuro area handing out a homeless newsletter and providing medicine when necessary. They're called Ikebukuro Renraku Kai, and I think are are in that it is run and organized by the homless for the homeless 自立 style. (As opposed to the numerous Christian groups in Shinjuku.) If you want to go patrol with the Ikebukuro Renraku Kai, show up Wednesday night a little before 9pm at the Metropolitan Exit above the escalators. They meet there before splitting into three or four groups to patrol different areas. I used to go, but now Aikido is Wednesday night..

In the Sanya area (near Minami-Senju station), which is has the most homeless in Tokyo, there is a branch of Mother Theresa's group, the Missionaries of Charity. A few Indian monks live in the facility, and with the help of dozens of volunteers they also have a regular soup kitchen and often give away bedding and clothes as well.