You still got paid for the destruction of their ship, though. Bounties are paid for results. As an LR I'm prone to dying (though I never do, any more, cause running makes more sense.) so whenever a ship of mine gets destroyed, I simply roleplay that whatever is left is hauled back to Alcatraz and recycled and rebuilt. Probably why Rogue ships look so dinky. I'm sure the Navy and Police forces have their ships rolled off the assembly line.
While its' not perfect... it does, I suppose work for most cases. But for people with special RPs like Mon'Star it doesn't make as much sense, not for 'one of a kind' ships/load outs. But we just have to live with it, that's the way Freelancer is unfortunately. RP is our only way around it, so lets just try be creative.