With a canopy on, the ute becomes a full bluff body, which has a lot of pressure drag. Without the canopy, pressure drag is slightly less significant, but not enough to normally notice (too many other 'noise' variables - wind speed and direction, gradient and condition of road, loaded mass of vehicle).
When towing, the boat is also a big bluff body, though it benefits from being in the wake of your ute. The bigger the wake of the ute, the less the pressure drag generated by the boat. A canopy will give your ute a bigger wake so it may help you. If you're so inclined, set up an experiment and tow your trailer down the same piece of road in the same direction six times in one day - three without the canopy, and three with. Change nothing else. Note wind direction and speed before each trial. Average and compare the fuel economy and top speed results. Sound like a lot of work? Have better things to do? Here's the easy route - fit a chip, and if you want to put stuff in the back of your ute without it getting nicked or rained on, fit a canopy.
Are your boat trailer brakes dragging?