Highly unlikely. Most of those security systems are passive listening for divers inhaling and exhaling and other sounds found outside of nature. Some do have active sonar "pinging". A ping every 10 or 20 minutes would provide little security value.

A dull thud sound was likely another boat or item in the water banging into the dock or boat. Next time you are in a pool bang something on the bottom and see how that sound travels in the water. A big plastic hull would certainly pick up that sound. Even a rudder flopping around can make a lot of noise.