I downloaded the linux 1.62rc1 yesterday and noticed the same thing... with very ugly circumstances. If I'm correct, then data in OXP's can override data in the core files. If you look at the hardened missile entries in aegidian-special.oxp versus the same entry in the core shipdata plist, you'll notice the yield is 12500 rather than 4500.
With the new collision code in place, this usually means instant death... at least for me, when encountering a hardened missile.
For the moment, I just removed the missile's dict entry and deleted it's corresponding equipment.plist file. Problem solved.
Now, if I could only figure out how to get my cloaking device back after my ship upgrade.