Hi Nos - is a possible solution to just leave the engine uncovered & down - the cowl stops the rain getting in & it will 'breath' as it would do normally.
Or can you cut the cover ( slits or remove areas to suit) where the air inlets are as this should allow the same ventilation as normal.
Possibly (although it'd be tricky) rig somehting to hold the cover off the cowl for better airflow.(maybe foam pipelagging ?) I've used an exercise ball -
in the bow of the boat , under the ebay cover , to stop water collecting / let air move around & left the area within the Aframe open- along the same lines ? ( can be passed to wife/girlfriend in the summer , however this carries a high risk of divorce/ seperation if not done very very carefully ! )
I'm sure most outboard cowls keep 99% of the water out - its hopefully what they are there for , but maybe like you it just feels better having every thing covered up in bad weather.