I don’t think these flaps were ever meant to “seal” the back end of the boat. If they were, I would have thought something like a neoprene seal around the flaps would have been used to prevent water ingress. I have also noticed the transom is slightly curved, so fitting a flat piece of perspex across the holes won’t seal them. But if you are going to try to make a seal you will also need to build up the hinge fixing on the transom. It may be worth trying something along these lines if you are really bothered with wet feet, but as I tend to end up wet when out sailing, I don’t tend to notice much coming in through the holes in the transom it’s what comes in over the gunnels I have to watch.