Subs in SH4 take 2 kinds of damage.
There is the systems damage you see in the damage control screen. In addition, the sub has a total number of hitpoints. The hitpoints are really the overall hull integrity.
The crush depth of the sub is a function of hitpoints.
If you see blinking lights, or leaks that never get repaired, it means that you took substantial hitpoint damage. This means you need to RTB, and try not to dive too deep if at all possible. In fact, stay on the surface as long as possible. In a harbor, you might have hit a mine or a sub net.
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