I use a high quality full cover (like a car cover) on my 2400 SC3 (the boat is kept on it's trailer when not in use). There is a support pole that holds it up in the center of the cockpit, and there are no low spots. The fabric is treated with something and water simply rolls right off, even over the seams. However, if snow accumulates on the cover and creates a depression from the weight a slight amount of water seems to seep through as the snow melts.
If there's no snow, only rain, it does not leak at all.