Indeed, it has virtually never been difficult to transport people, but many substances or sometimes devices have been problematic.
Having holds down below makes sense for seagoing things because of stability concerns: you can't go wrong with a low center of gravity. Well, okay, if you go too low, you might get nauseatingly fast roll, but that's not unsafe, just uncomfortable.
Having holds down below also makes sense for things loaded on the surface of a planet, because there's no point in moving the cargo any higher from the ground than absolutely necessary.
Neither of these would apply to starships, though. The two main concerns might well be ease of loading and (considering a starship supposedly typically doesn't haul cargo from A to B unopened) ease of access while underway. For the first concern, dorsal hatches should be as good as ventral ones. For the second, stowage at the same level with personnel ought to be preferred, chiefly because moving things horizontally is easier than moving things vertically when artificial gravity affects each deck...
In anycase, if you wanted to jettison something away in a hurry, you want the thrusters aimed at the ship, not off to the sides like an RCS.
Except that's not how the thrusters of an emergency escape system are aimed in real spacecraft... It's always off to the sides, to avoid flame effects on the thing you are trying to whisk to safety.
There's no real doubt the TOS-R artists wanted a rocket/explosive bolt scorching effect here, with four rockets/bolts indicated, rather than a random explosion of the thingamabob itself. Whether they did a good job or not can be debated, but mainly on artistic grounds.
On the general issue of this thread, the markings on the TOS ship, one aspect we might consider is the presence of the virtually same markings on the E-A. The two ships are of a rather different design; OTOH, the refitted E-nil and the E-A are basically identical save for the markings, but the former had no discernible features in the spots where the latter had the markings.
This might give weight to the interpretation that the various shapes and colors are abstract symbology unrelated to any hatches, seams or moving or immobile parts of the starship. Perhaps most of the painted areas are just aiming points for a Ptolemy
tender for an accurate belly-to-belly docking, so that a single key hatch will be properly aligned with its tender counterpart for transfer of fuel and consumables?