Lots of neat ideas in this thread for what those "thingies" might be.
Here's another one to add to the mix: subspace radio transceivers. We never really knew where Uhura's extraship comm traffic was conducted through, did we? Why not there?
It's entirely possible, though I have my own take on the subspace subsystem.
To me, on the TMP ship, the dark inset ring around the B/C deck superstructure is the main subspace antenna. A similar structure, inside of the hull, existed on the TOS Enterprise, just not exposed. I also put the "Star Trek V" ballroom at the front of the B/C deck superstructure, adjacent to this... which explains why the emergency transmitter would be in that location.
For the TOS ship, I have main communications at the front of B-deck, with the main antenna being an ovoid ring near the deck, ringing the entire deck.
This is how I explain why that part of the ship is shaped like a separate section... it's shaped by the requirements of the antenna.
I also treat the two little red arcs on the aft underside of the saucer as some form of antenna... likely the "backup communications" subsystem.
That's my personal take on this... but of course, all we know about "subspace radio" or real is what it does, in-story, so nobody else has to accept this. I can't support it, except as described above.