Reefers do have an insulated door under the outer roof hatch. At least that is how the 40' cars are set up.
I was charged to install a new roof walk and dropped a wrench through the open hatch. (note to self--close the hatch when doing this next time). Thus I count myself among the lucky few who are intimate with the ice bunker of a 40' car. (If you are going to do this yourself, I suggest a good diet plan, or getting a 6th grader to get the tool for you!). (Don' do this at home!)
The bunker is made of wire mesh, as I recall. There is a mesh bottom, held above the bottom of the deck several inches (of course the wrench fell through this too!). Below this is a galvanized drip pan with a drain.
As I recall, the mesh must hav extended across the end of the car, about 24-30 inches in from the end. Tight enough that you could not turn around down there.
The inner hatch was made by someone else (they were beautiful). I figure there was a wood frame with a soft insulation material, all wrapped in burlap. They dropped into the inner roof, plugging it tight. I don't know what good it would do to prop open the outer hatch without opening the inner hatch as you often see in photos. I believe the inner hatch was hinged on the opposite side, and you would see these inner doors flopped open on the roof.
Keith