Anyone notice how the second term is often used for the first? I think I’ve done it myself on occasion. OED has an earliest cite of 1976 for scupper in the sense of to sink a ship. It makes sense actually. Scupper, n., meaning a hole in a ship’s side, dates back to the 15th century but oddly enough when it was used as a verb (not until the 19th century it would seem) it was first as a slang military term for ‘to surprise and massacre’ and later more generally for ‘to defeat, destroy’, etc.
The noun scuttle too dates back to to the 15th century and means a slightly different kind of a hole in the ship’s deck or the side; the verb for cutting a hole in the side of a ship to sink her has 17th century cites. Other scuttles both nouns and verb - to run, a dish or platter (hence much later the coal scuttle), etc - are unconnected.
So the upshot seems to be if you want to use scupper for scuttle go right ahead, you have history and the OED on your side!