Ah, I remember this model from the episode of Mythbusters where they escape from Alcatraz. They used the model to test potential routes across the bay.
Yes, that's still open. It's now more of a museum than a working hydraulic model, though. The Corps of Engineers maintains it, but most of their analysis of the SF bay is done on computers. One of the big issues is salinity, as in how far up the Sacramento Delta salt water will penetrate during a drought. The physical model can't do salinity; the mixing doesn't scale linearly.