I'd say in general, aim for the engine room; stopping you target makes it easier to finish it off. Fuel bunker has a fair chance to get a critical hit and blow it out of the water; it's typically located just in front of the bridge. For warships, aim for the engine rooms and below the turrets; the ammo stores are typically close to the turrets.
For deckgun, aim below the waterline and put about 10 good hits in a compartment; that should get it to flood. Then target the next compartment, rinse repeat untill it sinks.
In stock this is almost certainly when ship HP reaches 0, in which case it really doesn't matter where you aim.
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