The weed hatch over the propeller is large but strong and has a well bolted flange rather than a quick release.
The box cooler for the engine cooling was another huge hole.
Note the stress relievers welded on the corners to mitigate the stress on the corners in the hull cut out. The tube stack is withdrawn through the cut out in the bulkhead on the right. The cooler box cut through a frame so the cut frame ends were fully welded to the sides of the box.
Patterns were made for the cone sections and transferred to the steel.
These were then cut and bent to the hull shape.
And the reason for all this fuss? Thrusters work so much better with a smooth flow. So with radiused and flat ends the water enters without turbulence and the efficiency is increased and the bag of nails noise significantly reduced. Thrusters work by sucking the boat rather than just pushing hence the need for a good smooth intake.
There is another hole to be seen in the photo above the thruster tube. The drain for the gas locker. This is supposed to be a certain size (according to a formula) to let the gas out rather than just be a drain for any water that gets in. So apart from a few holes for filler pipes and water drains and vents, eleven I think, that's it for the holes and none below the waterline.