[jabl]

> Also both of these (exhaust & intake) are not free to the inside of the vessel, but form a closed circuit with the engine, so there's no way to flood the vessel through those.

Don't know about this yacht specifically, but as I understand it a common solution is for the engines to suck in ambient air from the engine room.

> So probably we're talking about the engine room ventilation openings that would let water in.

Likely yes. And probably(?!) there were watertight bulkheads around the engine room, so by itself the engine room flooding might not have sunk the boat (assuming doors/hatches were closed), but if combined with other downflooding into the living quarters (doors, ventilators etc.) it would have accelerated how quickly it sank.