Multiple use drones have many advantages over single use missiles in a space battle.
The problem with small craft (missiles, drones, crewed fighters) is that their weapons are also small. Today, small weapons can do damage against large targets. In Trek, this no longer is true: targets have shields, and we have yet to see a compact weapon that would perform as well as the large weapons installed aboard big starships.
So a fighter or a multi-use drone is at a disadvantage: having to share its payload between multiple weapons or other systems means it may end up being below the threshold of effectiveness altogether. A one-off missile can dedicate all of its payload to a weapon that may stand a chance of actually inflicting damage.
In star trek effective weapons are relatively small.
Look at a photon torpedo; or at the size of a phaser emitter mounted on defiant/enterprise for confirmation.
If you have 50 smallish drones, each with a single phaser emitter of enterprise level, impulse engines and enough power to keep them running for 1 hour (not longer), you have firepower exceeding what a federation capital ship can bring to bear.