Since the units to which I refer have never been rented they are not included in the ‘vacancy rate’ calculation. One reason the vacancy rate is so low is that a not insignificant % of housing stock is simply kept off the rental market due to draconian tenant rights laws.
You only need to hear a few stories - such as the high school class mate who spent many $$$ and lost over a year of time - trying to get a renter out of her now deceased mom’s in-law unit before one simply doesn’t consider the parents house rentable.
The above includes the greater Bay Area and not just the 49 square miles of San Francisco.