"As Mytran has pointed out and I've got an image in this thread that illustrates the only two windows we've seen are in "The Mark of Gideon" and "The Conscience of the King". The insets in the cabins were never shown to have the outside stars which indicates just a shelf or some cabin inset."
I've tried myself to rationalize these insets as shelves, but each time I look at these, my unconscious tells me instantly window. As "Mark of Gideon" suggested, some outside windows do have shutters (compare to your post # 355), so what we are seeing here
http://tos.trekcore.com/hd/albums/1x06hd/muddswomenhd146.jpg
http://tos.trekcore.com/hd/albums/1x06hd/muddswomenhd395.jpg
http://tos.trekcore.com/hd/albums/1x05hd/theenemywithinhd141.jpg
looks like windows with shutters closed (below the flight deck given the angle of the walls) on deck 12 or lower.
Most interestingly, Kirk's (temporary) quarters are on deck 12 in "Mudd's Women" and so are probably Mudd's quarters (nice allusion: Who's in charge in this episode - The captain on the port or the captain on the starboard side?).
Spock receives the guests in the transporter room (deck 14?) and brings them to deck 12 via turbo lift or shaft 7. Now, according to "Enemy Within" turboshaft 7 is near "engineering" to the (temporary) quarters, but Mudd and company arrive from the other side. It appears Spock has taken them up to deck 12 but first showed them their quarters (port side) and took a counter-clockwise corridor tour. This is suggested by Kirk's order to the security guard to take Mudd to "his quarters". How does the guy know which quarters his captain is talking about unless this has (previously) been established?
If we seriously suggested, these windows were merely shelves, the inevitable question has to be why we don't see these (used as shelves) in later episodes and seasons? They were covered up with these Axanar Peace Panels or whatever these are (to hide Kirk's collection of porn?). To me it seems rather simple: Originally they had Kirk's quarters on deck 12 (and with windows) but then realized his quarters would have to be on deck 5 and there are no windows.
Regarding "Mark of Gideon" we all seem to agree that this window should be in the engineering hull. However, after Odana has collapsed in the window room, Kirk carries her straight into a circular corridor: http://tos.trekcore.com/hd/albums/3x16hd/themarkofgideonhd0872.jpg
Since there also is a circular corridor in the engineering hull according to "Ultimate Computer" I'm unable to believe in rationalizing options that ignore a circular corridor.
I'll take your last suggestion into consideration. Thanks for the discussion.
Bob