How do know he was awaken? Where was he and what were the exact circumstances?
"Jones said he and his wife were sleeping when they were awakened by knocking on the side of the boat."
The hour suggests a safety check was the justification and that they were looking for something else. There is a difference between 6-8 pm, and after 10 pm.
An El Al security specialist said that the Transportion Department's airline security check procedure was not effective save as a system for annoying people.
Coast Guard searches like this one - late at night as opposed to 6 am - 8 pm - arouse hostility and resistance by the law-abiding, and so are detrimental to real security.