Re: Self Bailing Deck - Ok to plug the holes?
I had an older Hydro Sports that had huge self bailing scuppers with rubber flaps, the hole size was about 3 1/2" or so. The deck was about 8" above the water with four guys fishing at the rear of the boat but in rougher water, waves slapping up against the back of the boat would take on water and if everyone moved to one rear corner to land a big fish, that scupper would allow water in as is dipped below the surface. I've seen the ping pong ball type scuppers, they look like a great idea. However when I owned that boat, what worked for me was to simply plug them while anchored and unplug them while underway.
Not having a plug that size I simply used two soft rubber balls that were easy to get in and out. (I used a towel for a long time before I finally found something better).
If your boat is that low in the water, I'd look into why, most boats with scuppers have plenty of freeboard and don't have a major issue with scuppers. Part of the problem on my boat was created by an increase in motor size. (I added a second 175 hp V6 outboard to make full use of the boats max hp rating). Prior to the motor changes, the problem was nearly non existent.
Saturated foam or water in the bilge can also create such a concern.