I suspect that is just the way the game is build. When you start a new patrol you get the default loadout. Just like you get a 100% patched up uboot as if it came new out of the warf.
A makeshift solution could be to add a certain nett-amount of renown to your total (in proportion to as many torpedos that were left at patrol end) before starting a patrol that allows you to 'purchase' them without loosing or gaining renown. But this requires manual intervention on your part.
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