Boats that are painted (Awlgrip, etc.) should be shrink-wrapped carefully to ensure that the wrap, its seams and tie-downs don't come into contact with painted surfaces, which could be damaged by abrasion as the cover moves in response to wind and temperature changes.
Since shrink-wrap provides such a good seal, make sure the installer provides screened vents facing in all directions to facilitate airflow. You'll want to have a door installed, as well. This way you can board after the boat is wrapped and open as many ports and hatches as possible for ventilation.