With what version of SH3?
Stock - You can always 'break their backs' by using a mag pistol and by setting the depth to 1 to 1.5m under the keel.(calm weather, adjust for different sea states)
Supermods - GWX or NYGM - This has been made considerably harder to achieve. The same still applies however you are not assured a one hit kill due to the changes in compartment hit points.
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