Are you going to topple over your game simply because every once a while, a weapon will deal more damage than it should? Anyway - usually, these things happen without deliberate intent of players involved, and they don't change the outcome that much. A host is responsible for identifying situations that constitute blatant abuse of this programming oddity.

My rule serves to discourage players who might want to use the simplest weapons in order to exploit this, thereby creating a completely unrealistic effect of "spears killing tanks", and paying too little in minerals and resources for a big gain in damage inflicted.

The second reason: the increased armor damage from many small groups of ships attacking one huge crowd of ships is actually a thing that can be reasonably explained. Since the Stars! battle board is two-dimensional, we have learned to view the battles as such. This is not the case, as the space is really three-dimensional. One can imagine ...