I was an active member of Hacker Dojo for the first several years. When it was still open to the public 24/7, we had a lot of the same problems. People do what they have to do to survive, and passing up a free roof wouldn't make a ton of sense. Figuring out respectful disincentives to that (or locking the doors, take your pick) goes with the territory.
And stuff did get stolen. We even had a rule that if you left things at the Dojo and they weren't obviously part of the facilities they were fair game to use, hack with, destroy, take home, whatever, just to set the expectation that there was no security (and to limit the whole "not sure if I can hack this thing" mentality). The high point on that was when some dude had a pretty nice position-tracking VR setup running on Windows staged in one of our large meeting rooms (he was one of the exceptions allowed since it was really, really neat) and the local BSD user group helpfully reformatted his boxes to FreeBSD for him. He was kind of pissed.
I don't think the Dojo was ever particularly comparable to Noisebridge, though, for better or for worse. I guess the Dojo was closer to a hackerspace than most other things you could call it, so it was as good a name as any. But the Dojo was more like a community center that had, as one of its facets, a hackerspace. Most of the people there were self-incubating startups or coworkers, not really people doing the kind of open, collaborative work that typifies other spaces. We had a community of people who were more like that, but it was a subset, not the place itself. Nowadays, the balance has tipped even more, and the coworking aspect is even stronger. At the point I left, at least, most of the classic hackerspace aspect had taken a real back seat.
Noisebridge, for all its warts, is something pretty special IMO.
He's right, and it's sad. Hacker Dojo today is a big room with bright industrial lighting in which people slave on laptops in silence. Under the new management, the lounge has been converted to a more upscale room with office cubicles for rent. Parking is now restricted to paid members during the day.
They have a shop workspace of sorts, but it's not used much any more.
The article doesn't mention TechShop at all. TechShop is still around, with three Bay Area locations. San Jose is in great shape, SF is in good shape, and the mid-peninsula location moved twice and lost members due to downtime. TechShop runs corporate team-building exercises for big companies; I've seen Google, Facebook, and Singularity University take over the space, pushing the paying members out. The big tools (laser cutters, water jets, CNC milling machines) are great, and I've used almost all of them. Not much social activity any more. There used to be Friday night events, but that died out.
Sadly, HackerDojo has lost its hackerspace feel, and it's much more of a normal startup incubator.
I attended both regularly in 2011-2012, and while my group of awesome friends formed from a kernel of folks from Hackerdojo, I much preferred Noisebridge's ambiance. It had more of San Francisco's zany vibe (including, to be fair, the occasional hobo), whereas Hackerdojo took itself somewhat more seriously as a sort-of-incubator in the heart of the Silicon Valley. The fact that HD's original digs was litterally a block away from Y-combinator contributed a lot to that.
One of the last times I was in Hackerdojo was when our group of friends painted the dinosaur mural in their new space (I'm still annoyed that the person who painted to book spines messed some up. No Bugsby, that messed-up K&R cover sucks :p). Nowadays, it's basically just a coworking space for stressed 20-somethings working on their startup idea. The guy who had put the arduino-etc vending machine recently took it back out.
I'd much prefer HackerDojo, at least there you can go pee and not have to worry about leaving your stuff.
Also, I read enough about their problems with drug use and the homeless who lived there, that I'd rather just not go back.