The vents are the outlets for what was the Astro ventilation system. In order to get air into the cabin of the car it is easier if there is an outlet for it as well. You dont say whether your car has air con or not. If it does these vents were blanked off. Whether it has air con or not the plenums under the outer covers had drain hoses that run out into the rear wheel wells, these hoses are rubber and could likely have perished as mine did and cause a leak. Replacement hoses are easily obtained, I chose to use plastic electrical flexi conduit instead because it will never perish.
The plenum could be filled with debris making water back up and then leak into the car as well. It would be wortwhile opening the plenums from the inside and giving it all a claean out. Up to you whether you blank them off, my car has had the air con removed so I opened up these vents permanently as it tends to get warm in the cabin anyway so every bit of ventilation helps.