From a source:
"..."that part about the transponder is true but the flip of a switch and its disabled, most large vessels I am sure are equipped with radar ,and do not need to use a transponder to detect even row boats and prefer to run in a stealth mode which we used to do it all the time; in fact, we rarely used the transponder because guided missiles can home in on it to within inches"
This person was in the Navy during the Vietnam fiasco and his ship patrolled off the coast. His Navy specialty was radio signal.
The lack of an AIS signature does not mean that these ships are not located off SF.