Hi,
As Designed by the Mod Creator (Lurker)-
From the Operation Monsun readme/release notes:
6. WARNING
When you return to port your sub "WILL NOT" have it's torpedo's auto reloaded.
You will have to load the torpedo yourself. This is to ensure that the "wrong" torpedoes are "not" loaded on your sub.
thread here:
http://www.subsim.com/radioroom/showthread.php?t=134922