Scuppers should not ideally be under water, they will still drain a little while under water, but slowly and not how you ideally want them to. If you stand in the corner and water cones onto the deck that is a problem, that should not happen at all. That likely means the scupper flaps are no good, and the boat is sitting way low. Sounds like I'd walk away even faster now with that info. Scuppers will be under water from time to time due to wave action, but if they are at the dock ALL the time, that isn't good, we all know Grady's can develop transom issues from water intrusion, if your scuppers and other Thru -Hulls sit below the water, they are more prone to this becoming a reality. Are the side thru-hulls nylon plastic or chrome over bronze, if plastic that is an even bigger issue. The side thru hulls should not be fully underwater, if at full laod they have water touch them, that is acceptable, but not how the boat was designed. If they do they need more attention, but sounds like yours are way below where they should be sitting, I know a lot of islanders sit low, but the one you are talking about seems a bit lower then the rest. I wouldn't buy that boat if it was the deal of a lifetime price wise, just my opinion.