Hello Iburess,
You should be removing and cleaning your exhaust elbow. Is it a down angle or a goose neck. Not sure what model Yanmar you have. If you notice restricted flow, check sea water intake and sea water pump impeller and cam. Get a Yanmar Work Shop Manual. A must. It is not often you have to remove the heat exchanger and have it cleaned." DO NOT USE CAUSTIC " That will eat your exchange and they are a pretty penny. You can buy the V-gaskets and O-rings and remove the brass end covers and take a look to inspect the tubes for debris. If the tubes are clear then change the coolant (antifreeze) and be done with it.
Happy sailing... Squid