There are probably a few control-freak carriers that won't allow them, but for the most part they don't care. My first van had rear windows, which of course I covered up. You want them covered because of privacy, and to keep people from seeing what you're hauling who might get a little too curious. Every now and then I'll see someone driving down the road with uncovered windows, but I have a feeling most of those are day delivery or couriers and not OTR expediters where they have to spend the night in a parking lot somewhere. An expediter with uncovered side or rear windows is just a break-in waiting to happen. Generally speaking, if a carrier won't allow a van with uncovered windows to be leased on with them, it's not because of the uncovered windows, it's because they are reluctant to take on an owner/operator who is stupid enough to have uncovered windows.
Now, a van with covered windows, which is what you actually asked about, is another story. That's not going to be much of a problem, except to the control-freak carriers who know how easy it is to throw a brick through a side or rear window and get to the freight. You won't see many with a sliding side window, since those are passenger vans, but you do see a few. You see many more with covered up rear windows. Those are actually pretty common.