It also depends on whether or not you prefer to play with the mech destruction option on. Personally, I always have it modded to a 90% chance that the mech is destroyed if the CT was taken out (similarly to the pilot survival roll, I like to have at least a chance of avoiding it, so that I can hope).Interesting that there is a chorus of "do not put ammo in the CT," but I have to say: having played for 86 hours now, I've only been "got" by this once, so I'm gonna have to disagree.
Chest is where you can put the most armor. It seems pretty obvious from the way the combats play out that chests get hit less than arms which get hit more than sides, which get hit less than legs. So something like: Head/Legs < Chest < Sides < Arms.
The point being: if your chest armor is breached you are near death anyway, and the difference it makes to have ammo stored there is--in my experience to date--negligible.
With those settings, I absolutely would consider having it happen once being one time too many. YMMV.