Flush hatches have been done, by me and others:
viewtopic.php?f=3&t=577&hilit=flush+hatchesI really like the flush hatch setup because it makes sitting very comfortable.
I followed this design exactly, and it "works", but with a caveat. It drains into the footwell, but there is often more water than the capacity, so it would leak into the compartment if there isn't a good gasket seal. Since you need a seal anyway, I've come to realize the draining part isn't very useful, so when I redid my Pocketship this summer, I removed that portion of it and now built mine exactly as specified in the Guider design by CLC: there is a small lip, with a gasket glued to it around the hatch opening. The door is completely removable. There are four swivel "hatch dogs" held down by through-bolts through the deck that hold the hatch door tight against the gasket. I haven't tried this design yet on the water.