In 2007 the SFPD estimated between 2,000 and 3,000 bikes were stolen each year from SF alone, and that number has likely increased significantly since then:
http://sf.streetsblog.org/2011/08/08/city-could-require-bicycle-access-in-downtown-buildings/Some studies have suggested that only 50-25% of all stolen bikes are actually reported to the police so the actual number of thefts is unknown, but for the whole Bay Area I agree that tens of thousands per year is indeed a very realistic and even conservative figure.
Any reason why you asked this question? Just curious.