I too like the idea that those windows that are visible (dark and bright) can or are used as sensor ports as well. (And that there are hidden, shuttered, windows on the ship.)
Perhaps the engineering hull gets more windows because the sensors have direct access to the power systems and if they really did need to break out in the primary hull/lifeboat all those extra scanning gear isn't necessary to the survival of the crew?
As to the "cutting power" in "Journey to Babel", the exterior shots from the original FX still had lit windows. Ditto for "run silent" in "Balance of Terror". The only time we see a ship with completely darkened windows was the Constellation from "The Doomsday Machine".