The bay area has a high concentration of wealth where average salaries are almost twice the rest of the country. Programmers there make $300,000 or more. That's a doctor or lawyer in other areas of the nation.
I don't think high vacancy rates are the problem, I think they are a symptom.
Most of the people in this thread are only looking at the bay area from the past dozen years or so. In 2002, the picture was much different. In 1999, it was the opposite of 2002.
When you've lived in an area for decades, you can pick and choose where and when you buy. If you just moved there for a job, you're stuck without that time diversification and leverage ladder used by the folks who have lived there for a long time and accumulated many properties.