And we still lack evidence that even great swarms of small ships would be effective against individual large ships. In "Preemptive Strike", a swarm soundly defeats a Galor class ship - but in "Sacrifice of Angels", several such swarms achieve little beyond annoying the Cardassians (which is their intended goal, but that's a different story).
The Prometheus from "Message in a Bottle" could well be a droneship, with two drones of tactically decisive size and a token crew of four for in situ remote control and supervision of the computer (I guess Starfleet does remember M-5). It could be a very effective weapon that minimizes risk to Starfleet crews. But it would not necessarily be a war-winner, as it could well be more expensive to create than a corresponding fully crewed unit in every respect.
What would the Dominion do differently the next time around? Well, they seem to have very loose sleeves full of extremely dirty tricks. They are not experienced fighters of wars (they confess to as much in "To the Death"), but they are expert frighteners and punishers. Most probably, they would skip war altogether and proceed directly to the stage of making everybody on Earth and other key worlds suffer and die.
Infiltration is a confirmed Dominion skill and capacity. Horrid bioweapons are their forte. It's difficult to see how Earth could stand a chance...
Imagine a ship comprised of nothing but an engine, shield, computer, weapon (phaser or photon torpedo or some combination thereof) and other ancillary systems (commo, sensors, etc). These would be the equivalents to the same technology that you find on the larger manned ships. So either the drones weapons would be effective or the larger starship's weapons would be equally inneffective.
Take a look at today's drones. They essentially fire missles that were originally developed for manned platforms with great effect. Just continue that advancement to starship drones (perhaps its the term drone that is adding to the confusion).