In a TRUE self-bailing boat, the deck of the boat is built above the waterline, and the deck scuppers are also positioned just above the waterline, so that any water will drain from the deck, with none entering the bilges or the hull, whether it's underway, or sitting at the dock. The only drawback is that you lose a lot of gunwale height, because the deck has to be built up at least 6" from the floor on the average johnboat.
As for the self-draining plugs with the flapper ends, I don't trust them, as trash can cause them to not close, letting water in the boat. And these don't work at the dock, because they're below the waterline, and there's not enough pressure against them to make them open and drain the deck.