Back to the original topic, if nobody minds (thanks to Peter's excellent proposal I can now enjoy TOS-R "Court-Martial" and watch these guys replacing a running light. Thanx!).
In his interview with Doug Drexler for the 70's posterbooks Matt Jefferies was very clear that in designing the ship (and the interiors) he was aiming for what he called the "Hornblower Effect" and therefore a distinctive (ancient) maritime touch.
Indeed, in the old sailing vessels cargo was stored at the bottom of the ship and therefore it is feasible that the bottom hatches do serve such a purpose. My favorite "Hornblower Effect" is the spherical antimatter container ("Obsession") which looks like an ancient canonball which - essentially - is what a photon torpedo is used for.
I should also add that I no longer believe the yellow circle
is a cylinder with probe launching capabilities. One of my friends gave me a lecture why to have a 360° launching cylinder that launches probes but does not launch photon torpedos.
Instead the probes should be launched from the same launcher as the photon torpedos at the underside of the saucer. At least this could explain, why the phaser control room has the same height as the engine room: Behind the separating wall there are racks with all the various and mission specific probes.