The mod removes expendable CMs from ini control, so the only CM affected by the ini are towed decoys.
It's personal preference as to whether you want torpedoes to explode on towed decoys, but I think it makes life easier for the FFG if they do. Considering that towed decoys could have access to the ship's power supply, it is possible that a towed decoy could produce an EM field strong enough to fool a magnetic fuze on a torpedo, so this may be the more realistic option too.
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