It's actually never the case in TOS that the ship would orbit belly down; it only happens once in ST3. The preferred TOS orientation is portside down, offering equal planetary views for the top and bottom sensor domes, with one or two occasions of starboard down and one case of bow down. Similarly, a bridge would be in equal jeopardy atop or below the saucer.
How is that? If your scanners indicate you come under attack from the planet below, it seems wise to be able to re-align the position of your vessel so your most critical part is still protected by some kind of mechanical shield in case you have deflector failure.
As for the TOS Enterprise
we do have expendable storage space at the bottom of the engineering hull, a phaser control room that apparently became automated during the evolution of the series, and a lot of uninhabitated space surrounding the center of Deck 7.
Still, there's something odd about the placement of the three supposed sensor domes. The small one atop the shuttlebay would appear to complement the one atop the saucer, but is unnecessary as the saucertop bubble has no blind spots of note. In contrast, the saucer bottom dome would definitely benefit from a repeater at the bottom of the secondary hull, but has none.
One might almost think the domes are dedicated weapons-targeting systems, the top and bottom ones being associated with main phasers and the shuttlebay one with the twin phasers seen there in "In a Mirror, Darkly" and on the refit vessel. Scientific sensors might be viewing through the "windows" on the sides of the neck, oddly placed (and curiously numerous) for portholes...
Maybe the dome atop the shuttlebay is a compensation for the blind spot of the saucer's bottom dome?
Of course it could be a dedicated weapons-targeting system, but then the next question would have to be why the two domes of the saucer serve the main forward phasers at the bottom and the TOS mentioned "aft phasers" have to do with a smaller and only a single dome...