Most boats that do have "above water line" scupper outlets do so through the transom, or just above the LWL below the bootstripe to address the staining issue.
Minimizing below the water throughhulls does have it's appeal......
1984 Fast/Nicholson 345 "FastForward"
".. there is much you could do at sea with common sense.. and very little you could do without it.."
Capt G E Ericson (from "The Cruel Sea" by Nicholas Monsarrat)