You know - this has been a rather humbling experience (ya..boo hoo, I can hear you saying...your boat ain't sunk).
But for all my sentimental blathering about the build quality of my precious Scout over the last few years, this episode has brought to light some serious design flaws I had never even considered.
1). The deck (or sole

) hatch is fastened by just one twist latch. Really, it should have about four to produce a really good seal considering the size of the lid. The latch itself is also constantly getting fouled by sand and grit so I'm tempted to leave it unlocked during the day and have done so on a number of occasions. An easy thing to forget come the end of the weekend. Even when locked down, when I throw five or six buckets worth of water on the deck to scrub it down, I can then usually get the bilge pump to cough up at least a cupful or two. Prolonged, unsupervised presence of water of any serious depth on the deck would not be good.
2).The hatch itself is too far aft - its rearmost edge is probably only 18 inches from the transom. It goes that far back so you can get at the bilge and livewell pumps. I'd much rather have a deck plate screwed down over them thats got a great seal all the way round and have a hatch lid that's smaller and located further forward. I don't need to lower a paddle horizontally into the bilge. Sliding it down and back there at an angle through a small opening would be fine.
Here's a topview from Scout's website of my Dorado dual console without the optional rear seat. What's interesting is the placement they show of the hatch is incorrect - at least for my 2004 it is. Mine starts well aft of the seat pedestals and runs much further back. This - as pointed out by Pascoe in that article - increases risk of leaking from any water that creeps forward from the scuppers. What you can see though is the inadequacy of that single latching point on a hatch of that size.
3). And I'm not sure what the answer is on this one - but I think maybe those scuppers are an inch or two too close to the waterline for real comfort. The problem with locating them higher though is that you would never get the last three inches of water out of the boat, unless you put the nose up under power and forced it out. At rest you'd either have to manually vent it to the bilge or use a handheld pump for the last bit.
Anyway, the only thing I can really do is look into modifying my hatch to add more latches. I'm just parnoid enough to consider adding one to each end, and two more either side of the existing one. That shouldn't be too difficult. It will be a pain to flip them all just to get a paddle out but I think it would make the boat much, much more resilient to leaking into the bilge and therefore, more seaworthy.