You can of course install a bilge blower with the idea of removing dangerous fumes, like your ski boat, but usually engine room ventilation on a Diesel
powered boat is for heat removal
, and to remove heat, you need the intakes up high, where the heat is.
It depends on if your after removal
of heat or explosive gases.
With the engine running and certainly if you have an exhaust fan too, there is a very slight negative pressure in the engine room, meaning of course the airflow is into the engine room and any noxious gases and heat ought to go out the exhaust fan or out the engine exhaust.
My boat came from the factory with a bilge blower mounted up high in the engine room and the duct exhausts out of the top of the transom so no heat is blown into the cockpit.
If your wanting to exhaust explosive gases like on your ski boat, make sure the fan is "ignition protected" so it can't be an ignition source