G'Day Greg,
You mentioned cockpit scuppers for drainage. Have you heard of Red7 bullet scuppers? These are by far the most efficient drainage scupper out there. the latest Red 7 models have a triple setup, I have an older model surf70 with a single bullet scuper and it drains like a beauty.
http://www.surfski.info/index.php?option=com_content&view=article&id=1035:hydrodynamic-aspects-of-surfski-drain-scuppers-or-the-science-behind-the-bullets&catid=49:tips-other&Itemid=131

i don't know anything about flatwater racers but it is my understanding that the upswept stern (below the waterline) on a ski is needed to allow the back of the ski to be picked up easily by a bump/runner. Some good footage below of " the Big O, Oscar chalupsky in a recent visit to Oz riding the bumps.
http://www.youtube.com/watch?v=gkcvIIC5aqg&feature=player_embedded
Cheers.
Love this topic