I rather think it would be a good idea to have a variety of ships carrying the prefix of a cruiser design series as this would create confusion among your adversaries (since deception isn't compatible with UFP standards).
...It would be even more clever to use a completely nonsensical registry system, and to change the pennants more often than the crew does laundry. Which is as good an explanation as any for the weird registries and registry changes we witness, come to think of it.
The logical extension of that is the realization that whatever the number of starships like Kirk's at the time of "Tomorrow is Yesterday" (or at least its unseen 23rd century "framing story"), "only twelve" is not
it! And of course United Earth Space Probe Agency has got nothing to do with Kirk.
(Quite possibly, Starfleet doesn't exist, either, and all our heroes are Klingons in disguise, whereas all Klingons are Earthlings in disguise. But that's not absolutely certain yet.)