I am having the same problem - ie leave port at mission start with a full load , sink ships have fun - then try to refit after what is invariably a mega schlep to a friendly port. I click the option to refit, the message saying "refit complete" comes up and guess what - no torps, no shells, no nothing
I am going to try the reinstall and am waiting for the 1.3 patch in case it is a game error - but I seem so out of my depth -geddit :p !! - that I wonder if I am missing some other obvious stuff....
Any help?