I believe they are the hot air ducts, air is ducted along them and up to beneath the windows. I still have mine, I still use the OTR heat, but many take them out. They are separate from the dash heat, and you can remove the OTR heat and still have the dash heat plumbed in. If you take them out and drive in 40 degree or colder weather, you'll need another solution for heat, dash heat won't keep up and a bus running at 60 mph in near or below freezing temps takes a huge amount of heat input to keep comfortable.
Brian