The only confirmed windows in TOS that I know of are from "The Conscience of the King" and "The Mark of Gideon". In TCOTK, the windows are approx 3' tall based on re-creating the interior as a virtual set. The windows don't match up to any on the filmed model although you could imagine them shuttered and thus not visible most of the time.
The TFF windows I'm a bit suspicious of due to their large size and lack of matching windows on the E-A hull. The way they are designed it doesn't look like they can be shuttered and hidden away which would require more creative thinking in how and where would they fit on the ship.