It's enough to compare the TOS Enterprise with the Galaxy class starship a hundred years later; we see the Galaxy has a vast and extensive lateral sensor array on the rim of the saucer AND the engineering hull, in addition to a ring of sensors on the dorsal and ventral side of the saucer. The TOS vessel has only those glowing domes on the saucer and one on the back of the secondary hull; those would seem to be inadequate for a ship on a mission of exploration IMO.
The dark "windows" probably contain optics/telescope elements intended to image distant objects across the electromagnetic spectrum, from radio wave through X-ray and everything in between. The lit windows are probably active scanners, some type of radars/lidars, spectrometers, and a few might even contain ordinary searchlights.
I might even go so far as to guess that the observation lounge from "Mark of Gideon" might have been a sensor bay that was intentionally left empty so it could function as an observation port. The sensor elements of the Enterprise would all be housed in those sensor bays so they could be serviced by engineers in a shirtsleeve environment.
Agreed on all counts. This also fits with the interpretation of the "ion pod" in TOS:R.