I have a check valve installed on mine.
https://www.westmarine.com/bosworth-sea-lect-in-line-check-valves-P011_332_003_515.html There should be enough resistance to prevent it from going in if the pump is not on.
Make sure the flappers on the scuppers are angled toward the stern. If they were put in straight up and down, it is easier for the water to get into the cockpit. I had the same issue last year and realized the tab was on the top and the flap caught the water as you drove along. Just my $.02.