I'm having just a little trouble understanding which hole you are referring to.
Your splashwell most definitely has a drain, and it is right above your drain in the sump at the transom. You can plug this drain, or leave it open. Mostly they are open. Your splashwell should catch most, if not all, of the water coming over the transom. If your splashwell has been removed, I can see water getting into your cockpit, as well as the appearance of a drain as you describe, right above the sump drain, and I would expect you to take water on into your cockpit.
You can absolutely get water intrusion through a sump pump that is installed to pump out low on the boat. In many cases a loop is used to keep water from accumulating (this is also done with wet exhaust) however this method is only as good as your fittings. They make check valves that can help in boats with limited space for hose loops. It ensures that the water only flows one way. Most use these to keep water in the hose, and avoid having it drain back into the boat after the pump shuts off. These installations are done low, near the pump, to hold as much volume as possible. This would also keep any water from backflowing into your cockpit through your pump. I'd caution you that I would not want a check valve to be a major part of the "floatiness" of my boat. They sometimes come apart and have nothing in the way of a barb to clamp the hose to on one side. In winter I remove my check valve so water does not freeze in my hoses.
I would absolutely install a bilge pump in my transom sump. I have seen way too many bilge pumps stop working to trust my safety to a single pump on a non self-bailing boat. At work I have several self-bailing boats and they ALSO all have at least two bilge pumps. There is nothing like a backup, and if you really get some water in there having the extra pump gets you dry much faster and that can make a big difference, and could be a determining factor in whether or not a situation is survivable or not.
THAT SAID, I have carried a fair bit of water in my cockpit. It makes the boat very very "squirrely" as a CD22 does not handle weight shifting very well. HOWEVER, I am astounded at how well these boats handle the extra weight in the stern in terms of overall buoyancy. NO reason to forego extra pump capacity though.