I'm also a local, long time sailor. There's been quite a few instances of big ships ramming small craft and no debris remaining. I don't know what the visibility has been offshore but here in Alameda there has been periods of low visibility (read fog) over the last several days.
The area between the gate and the Farallons is a major shipping lane with ships coming from north, south and west. They don't always stay in the lanes and they don't always keep a good look out. I've had some close calls with the bigguns myself over the years, and that's standing a constant watch. A single hander can easily get distracted or become ill and not see what is coming right for him.
As to taking the boat somewhere else, there's only a few places places within a reasonable distance: Half Moon Bay or Drakes Bay. I imagine the CG has covered those bases.
Unless the guy got a total wild hair and decided to go off voyaging without telling anyone, he's on the bottom.
I have to set this straight: I sailed there from 1967-'73. I haven't sailed in that area since then. I am sure freight traffic is intense by now---it was not a great worry back in the late '60's.
We used to do the race to Encinada every year for about 4 straight, and, out of Newport Beach, to Catalina quite often. No Sea Lions then to harass your transom.
I know where Half Moon Bay is...still trying to recall Drake.
It's still difficult for me to imagine a boat-destroying accident on such a good day and with such an experienced skipper, who has (had?) lifetime knowledge of the area.
I still suspect self-induced skullduggery.