Using the thicker plywood will significantly increase the weight of the boat. The deck will be harder to bend and the hull shape, which is dependant on bending the plywood, will be harder to get right. My advise would be to exchange the plywood.

That said, I have a Cape Charles 17 and it's a wonderful boat. It tracks well, it's fast, maneuverable stable and comfortable. It always suprises me when I get back in it after paddling other boats how responsive it is.