The USS Cole was in the middle of a harbor being refueled when it was attacked. Would putting the rest of the harbor at risk of autonomous craft justify a small bit of extra security? How many times have the US Ships put into port / refueled without getting hit? Just seems that it would be a way to spend a ton of money for something that overly complicates normal procedures, and only wards off that 1% of attacks. (Note, percentage pulled out of my rear)
Also.... any autonomous craft would surely need a remote control system. You can't stop the signal (Mal). It wouldn't be impossible for another country / faction to take control of said boats, and use them to accomplish their goal.
Basically, seems like a large amount of money for a system that would cause more problems than it would solve.