There are two ways to go here.
1) Accept that a magazine explosion is very likely going to cause the loss of the ship (I think that is probably the most realistic) .
1) Larger magazines receive additional HTK due to size (probably square root of size as with Shields), plus any additional HTK due to armouring. In VB6 all magazines are 1 HTK.
2) Larger magazines are more effective at ordnance ejection (perhaps explosion chance is divided by square-root of size). This would be used in conjunction with option #1 above. So for larger ships, magazine explosions are very rare but almost always catastrophic.
I would be in favor of all this. In my opinion, a magazine explosions should almost always be lethal. I have no problems however with large and highly advanced magazines having very low chances of explosion. So more HTK and better ejection systems for larger magazines sounds good.
In general I am always in favor of a small degree of uncertainty in combat. I think it really adds to the game. Consider these 2 cases:
1) I am 100% sure that the first 12 hits will not kill me so I can completely ignore them.
2) I am ALMOST sure that the first 12 hits will not kill me. But not 100%, so if I can I will mitigate/avoid/intercept them
The first case allows for "gaming the system" in my opinion, and lowers the tension. It is always, in my opinion, a lot more boring.
Instead case 2) really encourages you to stay on your toes. Always be cautious, never take the outcomes for granted, do not be afraid to use your "limited" resources like AMM to defend yourself. Field more balanced fleets, too.
And if sometimes things do not go according to plans, so be it. That is normal and realistic as well.
I also apologize if I seemed confrontational. That was not my intention, I am just very passionate about this
And I don't think C# Aurora will favor small ships, there's plenty of changes that favor larger engines, shields etc in the changelog.
EDIT: and Steve already went and listed the changes. I should have checked the new posts made while I was typing, instead I went and had lunch