That is a good question how can water be getting in if it's air tight. I think that swoosh sound you hear when unplugging your drain is normal. I hear it mine sometimes too. It does seem like it would indicate air tightness. Although I leave my drain plugs unplugged when the boat is not in use so that the hulls can breathe while it sits in the heat on the beach. I would recommend that for any Wave. That procedure also reduces any mold or mildew build up.
On a rough day I get about a gallon of water in each hull. Rather than having to lift or tilt your boat to get the water out of the drains I would recommend the Thirsty Mate
http://www.beckson.com/tmpumps.html It's very inexpensive and works fast and well. You would need a port in the top middle of your hulls, if you don't already have them, to stick the thirsty Mate in. I had eight inch ports added to mine. It was a small job and creates a nice storage area.
I think my leaks are from the ports underneath the mats that are used in the mfg process. I added new ones as the old ones looked a little warped and thought I sealed them real well but now I am wondering. My mats have become unglued and I just reglued them so that might help although technically those ports don't seem like they should leak at all if they are sealed right with or without the mats in place. It's an annoying thing. I took my boat completely apart and used marine silicone around every single fixture so I was surprised that I was getting any leak.