However, something else occurred to me. If magazine explosions can be this deadly, the solution would seem to be creating a lot of tiny magazines to reduce the potential damage from a single hit. That is 'gaming the system' but would be an obvious choice.
The discussion seems to have moved on, but I wanted to mention that I think, mathmatically, the result would be the opposite. If magazine explosions become extremely lethal then you'd want fewer, larger magazines, because any damage beyond what's needed to destroy the ship is irrelevant and thus decreases the
average damage of the magazine exploding.
For example, let's say a 100 HS ship has 10 HS of magazines, and the destruction of each HS of magazine would be enough to destroy 20 HS of internal components.
If the ship has a single 10 HS magazine, then 1 internal damage has a 1% chance of destroying the magazine (10% to hit it and 10% to kill the 10 HTK magazine). The explosion would "do" 200 damage, but in practice it only does 100 because the ship only has 100 HTK. Thus the average damage is 1; 1% of 100.
If the ship has 10 1 HS magazines, then 1 internal damage has a 10% chance of destroying one magazine, doing 20 damage. Thus the average damage is 2, 10% of 20. And this ignores the odds of the 20 damage hitting another magazine, which in this case would be awfully high.