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My group has always ruled that it depends on what is hitting the missiles and what kind of missiles are being hit. Basically, plasma missiles cook off any ammo that uses combustion or burning type damage. So, you can use them to blow plasma, HE, and fragmentation missiles/grenades. Fusion weapons, as per RUE, completely atomize anything they destroy: clothes, armor, weapons, and ammo. So in most cases, ammo hit by fusion weapons would just disappear before they actually got a chance to explode. Fusion ammo can't be cooked off by a blast since it is an electrical based reaction, like a fission bomb. However, hit it with enough juice and you can short out the electrical circuits causing it to detonate early. Fragmentation weapons can be cooked off, but have 0 chance of cooking off something else, unless it manages to catch the surrounding area on fire somehow. AP ammo has a very low chance of cooking off and cooking something else off since the majority of its damage comes from kinetic damage. Same thing with Slammer/concussion missiles/grenades. They do mostly kinetic and concussion damage. Unless the item is fragile, like those nerve agent containers from "The Rock", they have 0 chance of cooking something off.

Hope this helps.