When the engine is running, it should be sucking in enough air (which is simply taken from the engine compartment in small boats) to keep up good airflow. The real value with a diesel engine is when the engine is shut down, the forced air from the blower will cool it down faster, which prevents the engine oil from cooking and tarring, and taking the heat out of the boat keeps you cooler as well.
As an exhaust for the afterberth it might be excessive--engine blowers usually are high velocity and noisy. For a berth you are better off with a low velocity high area (i.e. large and slow) fan.