Clarify?
You may have to clarify your question a bit...If you are referring to the exhaust port on the transom, there is no cap that I am aware of. Some boats had a flapper, but most corroded and fell off.You should not have any problems with water entering through your exhaust (except perhaps is following seas). There's a high loop in the hose that prevents that.The common problem people discuss is that the water pump can fill the muffler with prolonged cranking. That water is coming from your INLET. It's the same water that always goes in there, it's just that without the engine firing, it doesn't LEAVE.Anyway, that's why there should be a drain plug on the muffler. You only need to drain the muffler is you are cranking away without firing. Normal operation does not require draining the muffler.What ever you do, starting the engine with the inlet closed is not recommended. Damage can occur to the pump if it can't suck water.