That's a great idea, thanks! I measured it out as suggested and the rise is subtle but definitely present.
I finally found the camber formula in Brian Lavery's book on Susan Constant, which confirms your suggestion: according to Thomas Harriot's ca. 1608 work, the camber is 1/2 inch for every foot of half breadth, or 5 3/4 inches for the lower deck of Lavery's reconstruction of Susan Constant. (The Susan Constant's lower deck scales out to just under 22 feet at widest, using an O scale ruler on the 1:48 hull section drawings.)
I think the next step is to make a test cross section of the deck to make sure the method I'm thinking of will fit the camber. I'm using thin scribed sheets of basswood, cut to shape using the template in the kit. The scribing runs lenthwise, allowing the sheet to curve into the camber and also providing a visual reference to the planking, so they will run straight. The sheets are narrow, so the center joint will be supported below by an additional sheet, which turns out to be close to the 5" scale height. A cross section a few mm in width, with planking, should show whether this will maintain the camber, and how high the deck will be with the various layers. I'll have to make the hatches, mast step, etc., before I cut the sheet for final installation, so it will fit over them when installed.
The quarterdeck will be where the beams come in. The 1909 replica, like Anderson's 1926 Mayflower, has a very short quarterdeck. It extends out from the cabin below, but not by much. A few old Dutch paintings do show this, mostly the work of Adam Willarts, whose paintings of the 1620s seem to have strongly influenced the 1909 reconstruction. However the majority of paintings, and more importantly, earlier ones, show extended quarterdecks, more like William Baker's reconstruction of Mayflower, and the modern replica of Duyfkin. The latter two have an open bulkhead here, contemporary artworks also show a solid one with two doors or openings. To support this, I'll have to build up all the stanchions (since the hull is reformed, the kit's pear shape stanchions are useless) so the arched deck beams will come into play.
The kit comes with very wide planking strips, annoyingly in fine walnut or something like that - just the thing you would not expect for a realistic deck. I bought some Mt. Albert scale lumber last night in 1x8" S scale (just now I find that Lavery recommends 12" planking, argh, so my deck planks are now slightly too narrow) and plan on using a thinned alcohol and india ink wash to get the greyed look of a deck. (From reading posts here, it seems that decks were not holystoned at this time.)
After reading a few issues of Ships in Scale, the camber story is very believable.