Was there some reason they built ships to have people poop overboard near the front, instead of toward the rear? Did they like watching poop float by?
Not saying it was used for this, but a potential application would be an early speedometer. If you know the length of the ship and measure the time it takes the poop to float by the length of the ship, then you can determine speed of the ship relative to the surface of the water.
So maybe it's called the poop deck because the people on the rear deck had a unusually keen interest in watching poop float by...