No kidding. Yes, the squirrel cage fan passes air backwards freely when it is not running. I suspect that the intake vents on most of our boats are not sized for modern diesels which need a huge volume of air both for combustion and for cooling. It is not easy to put bigger vents in and keep the original look of the boat. Tom Slane's vents look great and are made a lot better than the old ones, but I wanted to keep the vertical look of the old ones...
In his book, The Nature of Boats, Dave Gerr has quite a bit of information on engine room ventilation, including a formula to determine whether your boat has enough square inches of vent area. Having that doesn't guarantee that it is enough, but it is a step in the right direction.
One of his contentions is this: engine room blowers should be arranged so as to always exhaust air, never blow outside air into the engine room. The theory, I think, is that raising engine room pressure could conceivably cause odors or CO to get into the interior spaces if the exhaust system was leaky. I would think that having air blown INTO the engine room while the boat was running would be good- the problem occurs when you shut down. Blowing air into the engine room is not helpful in cooling it- you need to pull hot air out. This, in turn, would mean two sets of blowers. Too complex for me.
I suppose this all depends on whether the engines can pull enough air into the engine room while operating. If I were designing a boat from scratch, I would just use very large air intakes and exhaust blowers- plus maybe a set of fans to move air around when trying to cool the engine room after shutdown.