Take a look at this mod and see if it's one you can download and use.
http://www.subsim.com/radioroom/showthread.php?t=180921
Quote:
[REL] Unit damage from smoke and/or fires
Just as it sounds, now the fires on ships will cause damage and flooding. If there are enough fires and given enough time the unit will lose all HPs and either explode (die) or sink from flooding.
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IIRC it's a pretty small file, and according to the release thread should work with any version of the game including stock. Not sure why your targets are so hard to take down, but this might help a little.