You can download Ross Leidy's free Kayak Foundry software. It will allow you to manipulate the hull design, and will give you the changes in hydrostatic data. It's a wonderful program. The only problem is that I don't know how you would tell it to make a flat transom. The program is for kayak design only, and is designed for strip-built kayaks. You could bring the stern up above the waterline, and use the last form that touches the water as the transom, and since the stern is not in the water the hydrostatic data would be the same.

Like the others said, you are looking at something similar to a baidarka. The main thing is what lies below the water for your hydrostatic data, but there will be things to consider such as wind resistance above water, and weathercocking. I imagine a wave from the back would tend to push the kayak, and if angled may be more likely to tip it than to spill over the deck.