I'm not sure exactly how your ship building scenario goes, but you could make the buyable/flyable ships have zero armor. Then Gxxx an outfit that gives (at least) a single armor point On Purchase. (So they don't just blow up if the player accidentally takes off). That way, when then player captures a ship as their own (assuming they don't have the option to assign it to their fleet), their old ship will simply "self-destruct". Which could be explained to the player in the capturing dialogue. Of course you'd also have to Gxxx some armor On Capture as well, or they'd just blow up. Just a thought...
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Edited to add: Ok, a quick test reveals (as I'm sure you've already found out) that the AI doesn't take advantage of armor mod types. This would at least eliminate the need to Gxxx anything, just make ships with zero armor and have armor type outfits come stock on the ship.
(This message has been edited by slouch (edited 07-07-2004).)