You will not have a problem with a hurricane on the west coast Baja Cruise. Ensenada is only a very short distance from San Diego, and we don't have hurricanes or tropical storms this far north. If you were doing the Riviera cruise (mazatlan, cabo & puerto Vallarta) then hurricane season is the same as it is in the Caribbean. But you won't have to worry about that on Baja.
Most people who do not live here don't realize that every stop on that cruise is somewhere you could drive to within several hours. Except Catalina, which is only a one hour ferry ride from Los Angeles (san Pedro) Most of the time, the ship is just drifting at sea, as it doesn't take very long to get from port to port.