John, the only problems I would see are first, the danger
of flooding when the boat
is heeled over far enough to submerge an exhaust (which may be at a point where the water
is pressing against your hull
and ready to "climb in") and second, if the exhaust is upwind of the boat
, getting exhaust and monoxide problems on the boat.
The transom usually is in a low air pressure (relative vacuum) area when you are under way, and the exhaust helps reduce drag somewhat, while the low pressure helps scrounge the exhaust. Again, only somewhat. Mainly...you've really got to rock the boat to force water
back up from the transom, and anyone coming alongside never gets gassed.
Or you could do like the lobster boats, just run a dry stack straight up into the air, like a truck or bulldozer does.<G>