Supply ships would be stocked with torpedoes for resupply (from 10 up to 48) but U-boats limited in the number they received due to the time and effort involved in doing so.
This wartime interrogation report of captured U-boat men notes that U-boats would only receive 1 or 2 torpedoes in a typical resupply operation. Torpedoes would be floated from the supply vessel across to the receiving boat via inflatable rafts and life vests.
SOP was for boats to resupply on the way out, rather than the way in. They were just being topped off with fuel and torpedoes. Nothing like resupply in-game where you get a full load of torpedoes instantly.
You may be interested in this book. It's like the "Hitler's U-boat War" of resupply vessels:
http://www.amazon.com/MILK-COWS-U-Bo...1273484&sr=8-1 It's sitting on my shelf at home. I found it to be well researched and informative if you have an interest in this sort of thing.