I ALWAYS use scupper plugs on mine. If I leave them out for drainage, I end up with wet @ZZ. If I take water over the side, I just pull a couple out and let it drain, then put tem back in. With plugs in, I usually have a dry ride. I guess it all depends on what brand and model yak you have and the conditions that you fish in. If busting surf, I could see that you would want to leave them out.
MUCH cheaper option for scupper plugs.. Go to Academy and buy a pack of yellow foam practice golf balls. Drill a 1/8 hole straight through. Take a 9-10 inch piece of paracord, double over and tie overhand knot at two tag ends. Push loop end through golf ball and tie another overhand know right next to ball. Make knot as tight to ball as you can to create some complession on ball. it makes them watertight. You can make 6 scupper plugs for about $5. Cheap, bright yellow and they float!