The open auto racks will present another challenge in the fact it would be hard to "cheat",unlike a boxcar that You can "say" it's loaded. What I'll most likely do is use them as mt's for a scheduled run through .
I definitely recall seeing the totally open cars in the 1960s. They were mixed in with other freight so you do not need an entire train of them. I thought they were gone, or the sides covered I should say, by 1980 but every now and then in looking at my slides from the era I notice an open autorack that I never noticed before.
Someone wrote an article, cannot recall if it was MR, RMC, or the NMRA's Scale Rails, about using a strip of styrene or metal (the steel strip in a hanging file folder would be perfect for this) that would mount an entire deck's worth of vehicles so that the car would be easy to load and unload -- sort of like a shishkabob. Indeed I have even thought about using a skewer that could go right through the cars themselves. So the loading and unloading of a car does not have to be the pain in the rear that it might at first seem.
As far as vehicles themelves go, we are looking at three issues: appearance, weight, and cost. Something has to give there! Bachmann makes a set of five astoundingly ugly vehicles, in the Walthers catalog it is 160-42206, for $7.50. They are light. With some repainting and modest detailing you coudl fill a tri-level fairly cheaply and not have it become top heavy. And they are the sorts of model you would not feel bad skewering with that BBQ skewer or gluing onto that strip of plastic or steel as mentioned above.
I have NOT done this but another idea strikes me and that is to take heavy duty foil and mold it over a scale vehicle, trim around it, paint it a bright color and see if the eye could be fooled with a trainload of these mocked up vehicles. Again I have not yet tried this but it would have the advantage of being very light weight. Heh heh it would probably encourage you to run your freight trans rather fast so the eye could not focus on how cheesy the vehicles would look, but you could have a long string of bright shiny car-like looking things in your tri-levels.
Perhaps painting the interior of the empty foil vehicle with white glue would give it enough solidity that it could be handled w/o crushing it. Tires could be black construction paper with a dot of something for the hubcap. Or "real" tires I suppose. The goal here is to focus on weight obviously.
If that ends up looking just too awful, and it might, then I wonder about a fairly crude carved bit of balsa wood that would be shaped to look like a car, sanding sealer to make it smooth, and then painted with glossy paint. the glass? hmm Maybe silvery paint that would be masked? Not sure -- again I have yet to do this but I might need to try these ideas out when I start equipping my tri levels for loads/empties operation on the layout.