This is not a good idea for many reasons. Underwater exhausts are specially designed into the hull and have check valves and bypasses installed.
First, at slow speed, you will be increasing back-pressure on the exhaust which will increase carbon build-up and decrease performance. It will also make it harder to start due to the back pressure. This is why on yachts which are designed for underwater exhaust, there is a bypass for idling and slow speed. This allows the gas to go out the back above the water and sends the cooling water down under the vessel. At high speed, the back pressure is reduced due to suction created by the boat moving forward.
Second, anytime you add a direct connection to the water at the stern, you increase the chance for water ingestion. Don't even think about putting the boat in reverse. Any following seas that move faster than you could cause ingestion. If you are sitting still, anchored, or docked, even the wake a passing boat could force water back up the pipe.
Again, on yachts designed for underwater exhaust, the exhaust outlet is under the boat hull and not out the stern. There is also a vent in the exhaust that eliminates any siphoning action.
Third, an underwater exhaust will not eliminate smoke or fumes. Exhaust is a gas and is lighter than water, so the smoke and fumes will just rise through the water and you will still have it. You see this on outboards where the exhaust exits through the propeller hub. Plus, outboards are still loud even though they vent the exhaust out the hub.
The major advantage of an underwater exhaust on a yacht is to decrease the noise of splashing water caused by cooling water that is forced out of the exhaust. It also decreases the soot that builds up on the transom due to the station wagon effect of the large yachts moving forward.