By plugging your scuppers and not providing a way to allow for draining/pumping of water as I've read a few times here, you are basically just opening up the possibility of forgetting to unplug the scuppers and having the boat fill with water - without any way to pump it out as the water is trapped on deck (ie thunderstorm). That sorta problem could sink a boat if left unattended - as could low scuppers and say the current turning around w/ the stern into a current like we have in the Merrimack, a dock line a little too tight, etc..
Of course with trailer boats we get away with a lot since we are typically on the boat the whole time, but even my 17 ft skiff - I will tie it to a dock on occasion and leave it there for a day unattended. It's sure nice to not have to worry about that sorta thing, that one just drains into the bilge and has 2 pumps w/ 2 float switches - no stress at all with that setup.
Many small boats live in the water all season and do not have self bailing decks - it's really not a very important or effective feature with only a couple small holes, especially so if you restrict the flow of water (in an attempt to keep the deck dry) w/ flappers or one way balls, etc.. A couple good bilge pumps can bail just as quick, except instead of water rolling around on the deck after you took a wave over the side it will go down to the bilge - which is a much safer place to temporarily put 300 lbs of water in a small boat.
On the flip side if someone absolutely could not stand the idea of not having a self bailing deck and was starting to consider a new engine, a huge cost, as a hail mary to solve this problem (which again won't work): On the high end the easiest/lightest replacement decking material, pre laminated divynicell panels, would be < $2500 for this boat. You could raise the deck yourself for a lot less $$ and end up w/ a better boat (sounds like from feedback here there is room for this) or potentially pay someone to do it for not much more. If you are not the type to take on such a project (and I get that) - it very well might be worth calling the builder of that hull, asking what it would cost to see the deck raised 2.5 inches or something. It will be a huge cost, but if you love the boat that might be the sure fire method of making it just right, and the original maker is likely the one who can do it the fastest/least-expensive as they understand what's there 100%.