"Scupper - an opening cut through the bulwarks of a ship so that water falling on deck may flow overboard"
like so much other bullshit, this comes from the navy. can't just say tossed overboard, nope, gotta have a whole new nomenclature regarding gutters on gunwales to say the same damned thing as landlubbers
Well that's where it originated from. Scuppers on ships were the deck drains that let water that came over the railings drain back out.
A ship was deemed scuppered when it was so low in the water that water could now enter through the scuppers, which is a bit of a point of no return in sinking a ship. No bailing or pumping will help at that point.