Speculating about fictional technology is, as you said, a pretty abstract (though fun) exercise because one’s conclusions can’t be proved objectively one way or the other. Since, however, you’re disappointed by the fact that in the TOS TV series the Enterprise has glowy red nacelle caps but no glowy blue nacelle sides, and that in the first six Trek movies the Enterprise has glowy blue nacelle sides but no glowy red nacelle caps, here’s a speculative argument that might make you feel better.
If I understand correctly, you’re saying that the presence or absence of glowy parts on nacelles should be logically (to coin a phrase) provide as an index of technological progress: no-glow nacelles ought to represent the most primitive stage of nacelle evolution, two-glow blue-and-red nacelles ought to represent the most advanced stage of nacelle evolution, and one-glow (blue but not red, or red but not blue) nacelles ought to represent an intermediate stage of nacelle evolution. If we accept that premise, then yes the depiction of nacelles over several centuries of fictional Trek history makes no sense. But here are two reasons why the premise might not actually be correct.
First, the presence of a design feature on real machine A and its absence on real machine B does not necessarily mean that A is more advanced than B (or vice-versa). It might instead simply be because A and B are designed along different principles, in the same way (for example) that helicopters have rotors and airplanes don’t because they’re different types of flying machines. The presence/absence difference might also be due to specialized design/mission requirements that have nothing to do with technological sophistication in an overt sense. Take the MiG-25 Foxbat interceptor, which the West go to study up close when a Soviet pilot defected with one back in the 1970s. Publicly, Western analysts mocked the plane for having vacuum tube electronics. Privately, they weren’t laughing: vacuum tubes are more resistant than transistors to electromagnetic pulses from nuclear explosions and are more temperature-tolerant in extreme conditions.
Second, the lack of visible red glowy nacelle caps or visible blue glowy nacelle sides doesn’t necessarily mean that both glowy parts aren’t actually built into the nacelles; it may simply mean that, for some sort of engineering reason, they’re plated-over or shielded from view in that particular model. Take modern jet aircraft as an example. For the past several decades, we’ve seen some aircraft whose jet engines are mounted externally on the wings (like the KC-135 Stratotanker) and some aircraft whose engines are buried inside the airframe (like the F-15 fighter). An even better example would be the B-58 Hustler and the prototype XB-70 Valkyrie: both were American 1960s-era jet-powered supersonic strategic bombers, yet they look radically different because (among other things) the Hustler had huge external engine pods while the Valkyrie had recessed engines. Somebody who knows nothing about aircraft design might glance at the Valkyrie and think that it has no engines at all, or might look at the twin square intakes below the plane and think that it has two engines, and therefore conclude that the Hustler (with four highly visible engines) is more powerful. In fact, the Valkyrie had six engines buried in its fuselage, each of which could produce 28,000 lbf of thrust with afterburner, or 168,000 lbf in total. The Hustler’s four highly-visible engines could each deliver 15,600 lbf with afterburner, or 62,500 in total, which is two-and-a-half times less than the Valkyrie (which could fly at over Mach 3, in contrast with the Hustler which was a comparative slowpoke at Mach 2).