The Vents w/ flaps you mentioned serve several purposes based on brochures and other info. I have read though the years.

The first purpose was allow you to close the doors easier. When you close the door of the car with all windows in the up position, the flaps allowed air to escape reducing air pressure in the car and allowed the doors to shut easier. The reality is that the cars aren't that tight to begin with so the effort needed to close the door is probably not changed too much.

The second purpose was for flow through air when the vents were open.

The slit in the side rear trim panel on the inside of the car near the back glass was to help with defogging the rear window.

You asked if you should plug them up. I would not recommend it. If water gets in there it will have no way of getting out and will begin to rust the body seams in that area. The flow through effect helps dry any moisture that might get in that area.

Joe