[Suicide Junkie]

The main concern is processing time, of course... battles already take long enough.

A simpler version of that would be to have each ship list its current target, and how much damage it expects to do.
When picking a target, each ship would check the list, and not shoot at a particular target if the fleet already has enough firepower targetted on it. ("Enough" being determined by the strategy's overkill factor)

Then, if there are no targets left, the ship should decide whether to hold fire and wait for a good target, or just fire anyways.
Weapons with a short reload, and those with little to no ammo usage would be more likely to be fired anyways, while long-reload or expensive weapons should not be wasted.
How to specify the above fire/hold settings is left as an exercise for the reader.