Well, the thing is that, without a human pilot, larger ships are more inefficient, because of the 50% health cutoff.
Generally, ships go over the cutoff when destroyed.
This means that 100 25-block fighters can suffer more BLOCKS LOST than a 2500-block warship, while still having units active and capable of combat.
This is beneficial in combat, because as soon as that 50% cutoff is reached, ALL blocks remaining on the ship are no longer useful in drone warfare.
Overall, my point is that the person who continues fighting the longest wins. One large ship loses a lot more blocks if it's knocked offline, because there's more blocks that can remain intact while the ship itself is still in one piece. The 2500-block ship will lose 1250 blocks and then stop functioning, a complete waste of the remaining 1250.
100 25-block ships can each lose 13 blocks, leaving only 1200 blocks inactive AT WORST. Most likely, ships will be sent over the limit. However, this means that you can lose, before combat ceases, 2488 blocks, assuming that once a ship overheats its remaining blocks are considered "destroyed". Which, honestly, they might as well be destroyed.
TL;DR: Small drones are more advantageous than single large drones, because they are more efficient with block use/loss in combat.
So no, we will almost certainly NOT see any lone wolf win this Drone War, because they're gonna get destroyed by multiple smaller vessels.
If you want proof, try taking down an Isanth from the inside with a handgun, and see just how much of the physical armor and structure is left when you're done with the soft insides. It's really quite incredible, the amount of potentially functional systems a large ship will go down with.