Hi Aaron, the round containers Lionel has put in gondolas for decades, were modeled after containers used for carrying cement powder in gondolas. The Lehigh Valley cut holes into the gondola sides to assist in use of air hoses to remove the powdered cement. A model of that particular is below.
I don't think there was any deep thought put into those Lionel Crate Load sets, other than items to put into starter set gondolas. You'll notice the crate sides aren't straight, but at a slight angle. These items were I think really intended for play. Kids like to put things into train cars, and gondolas/hoppers make that easy. These loads were made for that.
Painting them certainly improves them. Using masking tape, I stick one open side of the pipes on a row of masking tape, and prime them with plastic safe spray paint. Then flip them over to do the other open side. Same technique for the small beams. If you try to spray paint them without sticking them to something, they'll just fly around.
If you have a Do-It Center hardware store, they have their own brand of spray pain that works on plastic. As does the Krylon brand sold at Walmart. The pipes and beams I spray paint a rust, silver, or some industrial color. I got several sets of them and use the pipes and beams for gondola loads.
For the crates and pallets, you could prime them and then either paint them with a light brown spray paint, or hand paint them with acrylic paints, which would allow a little more variation. BUT you need prime them first before you can brush paint them with acrylics.
