Re: is this bad?
If I understand correctly, when you are stopped, at drift or on the anchor, another boats wake or a swell will come over your transom correct. And you drain it moving and pulling the rear drain plugs and let gravity do its thing.
If it is an older boat, most likely does not have a self draining deck and the transom may not be fully enclosed allowing the deck to take on water, this is normal...pain in the ***, but normal. I used to have an 1982 18ft and it would constantly have about an inch or two of water in it...would have to wear boots. Yes, that is one way you can drain it by pulling the rear drain plugs while moving, but I just used to let the water splash around. Also, an 18ft is not really an "offshore" boat regardless what others tell you, especially the person who is selling it.
To me, one of the greatest inventions of the newer boats is a self draining hull...and of course the technology and application of the 4-stroke.
But to answer your question, if you have a fiberglass over wood deck (most older boats had these), the water will eventually creat soft spots and eventually rot out the deck over time.
