I know I'm on record on numerous other threads re: this topic but my preferred method is to aim for the aft or engine area (whether it be magnetic or impact setting).
The very least you can expect if the ship does not sink would be it coming to a halt, therefore making it a sitting duck for DG or a coupe de grace.
In a convoy situation the escorts would eventually leave it and get back to the job of escorting the convoy.
For those who want a hint where the sweet spots are (based on stock SH3) there is a file called 'shipchart' available from my sig.
