The "operator" doesn't have nearly the amount of control over things as you think. You can't get a subcontractor inside the port gates without having prior approval from the authority that controls the port itself and is responsible for its security, and it is becoming increasingly onerous for truckers, and container handlers from off-site locations who need to acces areas of the port to move these things around.
. . . learning the mechanics regarding which ships are likely to be targets for inspection based on observing patterns of how DHS and the coast guard operates, etc.
That's a possibility, but a terrorist doesn't need to spend $6.8 billion to acquire a major global corporation to get this kind of information.