There are usually tell tale signs, like the plugs being clean or rusty in those cylinders, or, if you pull the exhaust manifold off, you will see rust tracking in the head exhaust port. Sometimes you just see small beads of water inside the insulator portion of the sparkplug.

I've seen them where the leak was so small the boat ran pretty normally but just had an occasional miss. As the leak gets worse it can even get to the point where enough water comes in to hydrolock that cylinder or bank of cylinders, and if it sits too long (like even a few days) the piston rusts firmly to the cylinder walls.

I rebuilt a marine engine for a buddy one time, after it had sat for only a week since last running, and we had to drive the pistons out with a block of wood and a sledge hammer.

Don