I added extra torpedoes to my sub by doing CB's idea of changing the nodes for something else. I added the torps from a destroyer load-out and it worked. I made a point of firing all my bow tubes, then the extra torpedoes started to load:
Here is the bit I altered:
[Equipment 4]
NodeName=T01
LinkName=21TorpedoTriple
StartDate=19380101
EndDate=19451231
;[Equipment 4]
;NodeName=M01
;LinkName=NULL
;StartDate=19450101
;EndDate=19451231
I left the original in there by editing it out with the ;