If you'll recall from DS9's "The Search", the Federation (publicly) doesn't believe in warships, so it would logically follow they would not (publicly) believe in fighter-craft, either.
...And since they do have warships in practice (indeed, we've never seen a non-warship - even UFP hospital ships are armed!), it then follows that fightercraft should exist as well. As later demonstrated.
In contrast, even when a DS9 Runabout is so equipped, it seems only capable of severely limited firepower.
To be sure, we've not seen these craft being used offensively against hard targets. This may be because they are unsuited for the task - but plotwise we have failed to see such combat because Sisko's runabouts never really operated in an environment that would have had hard targets. Three of them were considered an even match for a pair of upgunned attack fighters, though.
Since photon torpedoes form one half of the Trek arsenal, and since these weapons are (at least in later Trek) portrayed as "conventional" self-contained projectiles, it might be that any craft capable of carrying them is also capable of firing them to the exact same devastating effect as a large starship. The DS9 Tech Manual suggests that the runabouts could indeed drop-launch a few standard torpedoes, which would then have the same effect as a volley of the same torps from a starship. This may be what we see in "The Search II" where Sisko destroys the wormhole with four torps coming from beneath his runabout. Voilá - a very destructive runabout
dictated by the Trek rules!
if (1: they could offer defensive abilities to deal with incoming fire, or face a high mortality rate without them; (2: they could employ as-yet unseen weapons technologies to make a fighter-based dimension to deep space confrontations credible; (3: these craft would also offer a non-military dimension, so that they would be useful for transportation and exploration.
The first two conditions could be ignored if the fighters don't operate against enemies that fire back, and if they don't fight in deep space. Indeed, the second time we saw these fighters operated up close, they attempted to attack an enemy that would not fire back much, and would have done so deep within a star system.
The third time, they attacked a capital ship, and everybody indicated that this was frighteningly wrong.
That these fighters were part of a group that attacked a lone capital ship in the first appearance, in "Preemptive Strike", might be another special case. The Cardassians were surprised (or then just outraged) that the small craft possessed heavy weaponry, such as "type 8 phasers"; perhaps the attack was only successful because the Maquis had special weapons for the opening salvo of their ambush, a bit like a bunch of speedboat pirates packing a torpedo in one of their boats for stopping the opposing frigate, in addition to the usual MGs and assault rifles and grenades and light rocket launchers?
Since we never saw such as class of craft deployed throughout TOS and the 23rd-century movies, it's safe to say the technology made such a concept impractical for that era.
We never saw war in TOS, though. Except for "Errand of Mercy", where we had good seats on an apparent side show...
We never saw a dozen other things in TOS, either. Perhaps Starfleet/UFP has special technologies and doctrines for dealing with planetary evacuation or for mining asteroids or for dispersing nebulae. But since these things didn't happen in TOS, we failed to see the technologies and doctrines. We saw virtually nothing of the UFP in TOS anyway, since our heroes were operating outside that realm. Basically, they also operated outside Starfleet, save for a select few cases where bureaucracy caught up with them or a fellow starship (similarly far away from home) was encountered.
Despite hundreds upon hundreds of hours of Trek, we still lack a complete view. We could easily drop something like Starfleet Marines through the remaining holes, despite us already witnessing a major multi-year war.
Timo Saloniemi