The difference between the nacelle strut windows and the pylon neck windows is that the nacelle struts are never lit - making it easy to explain them away as something else (flush vents etc). The pylon neck ones however are lit, and in exactly the same way as the other windows on the ship.
Unlit windows in the nacelle pylons could mean no one is in there. The Polar Lights TOS decals do show unlit windows in the neck and engineering hull, too, if we dare call them "windows," that is!
BTW, there's the orange window (or, whatever it is) on the neck that I mentioned earlier.