I never thought of having a window be a weapon port, but why not. Or, as with torpedo tubes on a submarine, phaser hatch covers that are flush with the hull could be anywhere, with the seams too fine to see. The door swings open, the phaser fires, and the door closes.
Yes, that's true, even though I prefer there to be some kind of port so that something on the exterior of the model represents the equipment, which makes presumed windows good candidates.