It can take a few hours til the ship finally sinks. Lately I have been a bit more patient (or hunted by escorts long enough) to have to wait for a ship to sink up to 4 hours. Sometimes they don't sink even after that time. Sometimes they even seem to repair their engines and resume their voyage. But you have to stay close, as ships don't retain their damage, either after leaving the render range or the 50 km range (not actually sure).
Also, sometimes the game credits the sinking to storm damage instead of flooding damage done by you.
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