Wait for a 2-stroke guru, but I believe it has to be coming in through the exhaust and then flooding the engine.
In theory, this can not happen as long as all the normally sealed areas are sealed. Such as a head gasket for example.
The mere fact that the boat is in the water, water WANTS to get into the boat due to hull displacement and atmospheric pressures. This is the same principle as to why boats float. They float as the water can not enter the hull,,,
In your case, the water is entering the hull, (all be it through the engine apparently). There are baffles in the mufflers that can fail, but I do not think this in itself will allow the water to enter the engine. However, if you have a bad head gasket I could see how it would.
It is much like you holding your finger over the end of a straw and putting the straw into a cup of water. No water will enter it while your finger is on the top, but lift your finger and the straw fills up...