When there is no evidence of window at all, it would be for ducts or other infrastructure as already pointed out.

You occasionally see an older plane with a widow hole that appears closed over on the outside - I have always assumed that is because of something like a galley directly on the inside. I suspect that with the way they need to be able reconfigure the interiors these days, removing windows like that isnt done much any more or than for private jets.

I did once have the "pleasure" of getting a window seat without a window and hated it. I love looking out and taking pictures!