The Not-In-Universe is the trope of "Shape identifies fleet." This trope is VERY common in Sci-Fi, being obvious in Battlestar Galactica (Old and New), Buck Rogers, Star Trek, Star Wars, the whole Mecha Anime subgenre, and more.
Gene Roddenberry, according to multiple sources, said the ships must have two nacelles, with nothing between them, and a saucer; they may have a secondary hull. All of the filmed TOS ships match this except for the Tholian and First Federation ships.
In universe, it's reuse of known strategies of ship design.
This can be seen in how the last several US carrier designs are pretty much externally identical, in ways that go beyond mere practical considerations. Elevator locations, cat and arrest gear locations, and defense systems are practical; tower shape is far less a practical matter. Much of what's in the tower could be relocated, making for a smaller, less imperiled tower.
The Saucer design provides a low frontal cross section, and high deck surface. (Ignoring the illogic of having thrust run along the decks, of course.) A tubular secondary hull is similarly efficient, but puts more vertical space together than horizontal space. All federation designs seen save 3 mix these elements; the other three are special cases (the Multi-Vector Attack ship, the Warp Shuttle in TMP, and the freighter in TAS).
Further, the use of similar pattern nacelles means crew familiarity with them... likely, they also carry the same drive systems in them.