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First you will want to make the brass thru-hulls are properly in place and free of perforations.

Next check to make sure they are sealed properly.

Finally check to make sure all of the scews going into the deck and hull are properly bedded with some caulk and there is no swelling occurring in the area around them.

I would also walk the deck with no shoes on and move around on the balls of your feet and feel for flexing of the floor.

All of that said, I would put money on that fact that you will find moisture in EVERY whaler you look at. That said it is nothing that worries me any more. If I am looking at a Whaler and all checks out I typically will have the hull floated to check where the waterline falls. If the hull seems to float well I am typically fine with the boat. There is no set flotation level for any Whaler just a well trained eye. If it looks stern heavy and there is no apparent reason for it, the hull is probably holding a bit of water.

Follow this link to find a survey document I wrote up. It is at the bottom of the page.
Finding and Surveying a used Whaler