Aerodynamically, it's worthwhile to have all those openings closed.

Are you going to cover the airplane with UltraCote or Monokote? If so, then you may wish to do that first so it can be wrapped into the openings.

You also might consider using clear UltraCote for all those windows. Cover with your color film and then simply iron on a piece of clear over the whole set of openings. It's almost zero weight compared to hard plastic (which isn't going to weigh much, but everything adds up), but is about 1000% easier. and neater. and can't cause a mess.