When have we ever seen those features simply disappear?
Never. Which is why it's up to us to decide whether it would be possible for them to appear
, e.g. when Kirk opens a shutter in "Mark of Gideon"...
And those small rectangular shapes, some lit and some dark, all over the saucer and the engineering hull? Also windows. They were meant to look like windows. There were designed to look like windows.
Indeed. Things only get compicated when the "window" is of an odd shape or size (say, the big square things on top of the saucer rim, or the three big circles at bow). But those are probably windows as well, again because it would make little sense for a random selection of sensors to be "dark" while it makes perfect sense for a random selection of windows to be.
Windows that double as sensor ports sound extremely awkward,a s they would perform poorly in both roles. If there's sensor equipment there, it has to be close to the window, leaving no room for the alternate use. Or it has to be moveable, which is extremely awkward: the sensors should be in active position about 99% of the time, waiting for the unexpected, so it would be difficult to justify moving them out of position, like, ever
. And what sort of a sensor would emit yellow light? (Well, the sort housed behind the three large domes of the ship, of course, but that's a different shade of yellow from the one seen behind the windows.)