Welcome to the forum Jambo
I would consider the following.
The first thing required is going to be a real time comprehensive sensor suite. I would probably start out by just monitoring the key points until I had proved the system.
Vibration sensors/ transducers attached at key points through out the ship, preferably isolated from internal noise caused by normal crew activities, walking along gangways, slamming bulk head doors, etc. They would also need to be positioned where the vibrations from the movement of water out side the hull was at a minimum.
All the major mechanical points of failure would need to be monitored, prop shaft bearings, gearboxes, valve covers, etc.
It would also be helpful to have a digital map of throttle settings; engine vs shaft rpm’s, rudder angle, etc. If a real time analogue/ digital output/ diagnostic ports are not available for the ships controls then high resolution CCTV cameras can be used to visually read analogue gauges and controls. The more data you can accumulate the better.
All the data will then need to be filtered and run through a Fourier transform suite to isolate the various frequencies the ship produces under varying loads/ conditions. This would help remove resonance/ harmonic signals and accumulate all the data into one stream/ format ready for analysis.
I would design the system to produce a literal image/ picture of the data stream that could be recorded for later analysis/ comparison if required. This would also provide the data buffer required by the system to detect frequency changes over time, regular periodic knocks, etc. The recording buffer would also help alleviate a lack of computing power available on board the ship (I presume laptops) for real time analysis.
A single sensor data trace over time would look similar to this, the unfiltered regular knock at 1.8 Khz would be obvious to both a machine and a human, especially if its run through an intelligent Fourier filter (below). The sensors normalized profile taken over time can be seen by the trace on the lower right. Any signal that doesn't match the learned profile breaks through and is noted.
Once you have the data stream you can either apply a standard threshold analysis to highlight differences in frames or use a neural network to learn the regular patterns and highlight differences.
Neural networks are usually designed to find regular patterns; you just need one that highlights exceptions… to let you know if it’s not recognising the data stream.