Cordura isn't waterproof. The spaces between the yarns are too large for the coatings to bridge the gaps, so for uses like wear patches on high-tech rainwear it has to be backed-up with a membranes or other, tighter weaves of coated fabric. On a boat, varnish isn't going to fix this and may even be repelled by the fluorocarbon water repellent treatment that the cordura fibers are saturated with to help the coatings do their job as well as they can. If you haven't noticed, cordura also isn't even close to being smooth textured and would create substantial drag.
You might be able to coat it with epoxy, filling the weave and sanding the resin smooth as is done on strip canoes, but it would add weight without adding any strength and the unreinforced epoxy coating would be pretty brittle. Both the epoxy and the cordura would then be subject to U.V degradation and the only way to protect them would be very regular maintenance and recoating with a high quality U.V. absorbing varnish.
You could probably coat it fairly successfully with liquid Hypalon, like people use on skin-on-frame kayaks, but as far as I know the stuff isn't clear and would obscure the pattern. Stretching the cordura wouldn't be a problem. The fact that it stretches a lot (especially when wet) might be.
All in all, the idea is VERY risky and five years later you'll probably be trying to figure out how to get the damned stuff off in preparation for attempting to canvas it properly - if it even takes five years. The best option by far has already been given here, which is canvas the canoe normally and paint a camo pattern on the canvas. Another would be one of those camo net and/or fabric covers made to cover the top side and drape all the way down to the waterline in use. At least you won't be trying to figure out how to peel it off without ruining the canoe a few years down the road. Customers come up with all kinds of ideas when you are building them custom products. Some are good ideas and quite possible, others are not. Put this one in the "are not" category.