Richard, grains of all sorts were shipped in boxcars, including corn. But the corn was husked, shelled and dried before shipping. All photos I have seen show the dried kernels being loaded into boxcars. Boxcars were used for shipments traveling some distance, ie to a large terminal elevator, or a river barge, or to a port for overseas shipment.
The one exception where corn with the husk on was shipped by rail would be shipments of fresh picked corn going to canneries, but that would have been in open gons. Much like a farmer hauls corn with husks in open wagons. Corn canneries were equipped with husking sheds where the husks were removed as part of the processing to can corn. And canneries would not be receiving dried corn.
Of course practices today are quite different from 50-75 years ago. Today the only corn that is not shelled as it is picked, is sweet corn or seed corn. And both are specialty items going to local processing facilities the same day they are picked.