I'd vote to go for it!

There are a lot less strips in the deck than the hull and less tough curves and angles to cut. I don't think it should add that much time to the project. It will add a little to build forms to assemble the deck over and I think I'd shy away from the hard-chined pygmy deck profile and approximate it with smooth curves. Think about cutting 8-10 temporary deck ribs to fasten strips to. Also adding a sheer clamp, first to fasten the temp ribs to and then to glue the deck down to. I'd look for a sheer detail like Ted Moores Endeavour kayak has. For the deck ribs I think I'd shape them by eye and trial and error and do the final fairing on the boat with temporary strip as battens