They inflicted surgical strikes on the enemy fleet, though it's very difficult to tell how effective they were. They were a distraction because they were intelligently controlled and coordinated, which is impossible to do with an unthinking missile.
That's putting it generously. Nine waves of nothing and a foe whistling and twiddling his thumbs points to
ineffectiveness. The distraction was only a distraction because the tools being used couldn't do anything more. Actually starting to clear away the offending ships would have been far more conductive to the objective at hand, and Sisko didn't need to sacrifice sentients (at least not initially) to do that.
With the expert systems they can whip up, autonomous 'intelligently controlled and coordinated' is not beyond their capability. If anything, their computer technology is overkill when it comes to replicating the brain-dead tactics of the average human.
ST is in one of those positions where their technology allows the hot-seat, tips-of-the-spear units to be totally automated and tactically autonomous. The planes of contact should be dominated by the speedy decision making cycles and reaction times of computers. This is where the missiles come in: they only need somebody to designate something (or a potential group of targets) to hit.
Which is what the humans do, sitting somewhat further back where milliseconds don't mean the difference between hitting/outmanoeuvring and being hit/outmanoeuvred, and where human creativity actually has the time to generate qualitatively superior decisions which aren't based on totally out of date information.
Assuming that one demands we keep to the conceit that there is no way that an expert system can practically match a human intellect.
To use a different example, look at the opening fight from "Preemptive Strike." The Maquis had Gul Evek's ship easily outmatched and presumably ambushed it. They eliminated the Galor's more powerful weaponry as an advantage through tactics.
Interesting example. If the draft script is correct, the Maquis used their craft essentially as missile busses, and apparently didn't have enough missiles to finish the job outright. After which they reverted to doing the sort of graceful passes we all know and love from the War.
As for how they got the one-up on the Galor, there's nothing there to suggest it had anything to do with the attack being mounted by small ships. I'd wager that the Maquis simply took advantage of the classic Trek handicap: slow reaction time of their target due to a lack of automation. (eg. It takes ten seconds for the sensor officer say that unknowns are inbound and the watch officer to start going on alert... which by that time its all over.)
That's the key difference for me. Missiles are largely single use weapons, and in some instances they might be a better choice. But fighters are multipurpose craft that can handle other missions. It's the same reason we use fighters as part of our defense today, instead of simply spending the same resources on lots and lots of SAMs.
This is where the 'large number of smallest viable interstellar warships' comes in. For example, the Klingons had the spirit of the idea with their Bird-of-Prey. Although like the Defiant, the practical implementation still needs a lot of work.
The only role that that concept would have problems fulfilling is close air support. If ortillery isn't good, then that's something to be left to a specialized design carted to the field in an assault carrier.
Besides, even if we accept that a Trek warship can so easily target and destroy enemy small craft, it could do the same to a swarm of missiles.
Not a problem. At the least, the same job gets done without needlessly expending expensive personnel.
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There is, of course, a matter of unmanned strike craft. At least in fleet action, I'm not sure if that actually makes things any more efficient, unless any supposed increase in range and speed can't be accomplished just by making the missile a little bigger or something. The same idea might be nice for a CAS aerocraft, or some sort of expendable scout (optimized for speed, comms, and eyeballs, not for fighting, comes back if it can.)