physics
Being an automotive engineer type nerd I have to jump in.
Force of drag = 1/2 * rho (air density) * Cd (coeffient of drag…shape factor) * A (frontal area) * v**2 (velocity squared).
Assuming that you are driving at same speed in similar atmospheric conditions then you will get better gas mileage if the canoe improves your shape factor enough to offset the increased frontal area. A canoe could indeed help smooth the airflow over the rear of a vehicle…the aerodynamically messy area. It sure seems plausible to improve gas mileage is some cases (like a pick-up truck) and someone should contact Mythbusters.
Physics / fluid dynamics anyone?
All other variables being equal, it is essentially impossible to get better gas mileage with a canoe on a car vs. without. Might have better luck exceeding the speed of light or time travelling. As above, “other” variables are clearly involved.
Sounds like a job for MythBusters 
It’s The racks?
I have always thoughr a canoe on top of a car without the arodanamicly messy racks and bars would be ideal,but I never was able to get the boat secured properly without racks.It moved in crosswinds and when trucks passed,so I went back to my rack.
Turtle
Like WWW says…
Changing the drag coefficient and velocity. You are definitely affecting CD. Would almost bet you are driving slightly slower with boats on top for safety reasons. Not all vehicles will be positively affected, some will suffer a CD loss.
It seems illogical at first. I have no doubt these folks are observing some gains, same as I do not doubt some folks will lose mileage.
Mythbusters would have to try an array of vehicles and canoe sizes. This would be pretty expensive but interesting. Just don’t let the Gov’t run the experiments or will lead to vast new regulations regarding boat and rack profiles and materials.