I still think that if Explosive damage type was a bit better at getting armor broken down and a bit worse at getting killshots at an exposed hull, it would be a step in the right direction. The damage types have been drifting further apart into extreme specialization, and I think it's compounding the issue with paired weapons, especially THAT set of paired weapons. And right now, because of this, a ship with armor stripped either takes almost instant death or almost no damage at all, and gatling/flak hasn't so much become the preferred strategy as it's become practically the ONLY close-range strategy. This game is so unique and interesting in part because kills aren't GOING to be lightning-fast like in so many FPS games nowadays and instead calling for a lot of interaction between everyone involved... but lately, the kills have been getting faster and faster.
Assuming that explosive rounds become a more generalized damage type, ships that are unable to use paired weapons now have a better chance at being able to get kills or finish a ship on their own power, piercing weapons stop being a strict requirement and accelerate the process instead of being a requirement, and the flak finisher is still able to deal big chunks of permanent hull damage at once without bringing engagements to an all-too-rapid close.
And that last point I think is perhaps most important of all. The fact that we have a hullbreaker type and an armor piercing type means that a ship becomes vulnerable very quickly and vulnerability is a death sentence for many ships; to be honest, I don't think that a single armor break (assuming a fast and dedicated response) should be enough to conclude a battle.
Or if that's too far gone to consider at this point, give the gatling a much longer reload time, give the flak a slower firing rate and a slightly faster reload time. Make it so people will want to actually fire off a few flak shells instead of holding their shot for the inevitable (and very reliable) armor break, and so the flak cannon can't dump all its damage in the span of a second or two.