There were still some wooden-side boxcars running on the Nickle Plate during the last years the Berkshires were running. I'm not from the Midwest and the Nickel Plate wasn't a prototype that interests me, but I try to pay attention to what's behind the tender when I watch railfan-oriented videos. My thanks to the old-timers who shot movie film back in the day and the people who subsequently transferred the images to video.
As for me, I'm modeling a ten to eleven year period stretching from the late 1930's to the late 1940's, and there were still a lot of wooden-side boxcars as well as reefers operating back then.