First off, I just blew through this entire thread in one go. . . So, I apologize if I missed something, or misread something.
I'm all for catastrophic magazine detonation. I think it needs to be in there, a rare chance, depending on your ship design and technology, but a real possibility. And since magazines, generally, are associated with big explosions when damaged, or even just lightly touched with any kind of abnormal amount of energy, I feel like its a good place to apply the risk.
As well, the 100% warhead damage seems reasonable.
My only question(s) is this. . . Does the location of the explosion matter? Is it damage on "nearby" components? or does it move through the ship?
If it's not a question of location, could it be? Is there some kind of formula we could use to determine a probable "blast radius" inside the ship. If X number of Y strength missiles detonate, a size Z explosion is applied to A number of components. Or, perhaps that's already how this is working. . .
Edit: Thinking about that, I realized that, at least with most of my larger ships that might actually survive a major explosion, there are MANY small components. Mostly engineering spaces. Which means, I'm not good enough at math for this.