I think the exaust has possitive pressure when the engine is running which would prevent water from entering. OTOH water entering the engine air intake.. would be quite bad for the engine I guess, so there'd be protection against that. 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.
So probably we're talking about the engine room *ventilation* openings that would let water in.