As far as interviewing surviving merchant marine guys (their target) I haven't run across any stories of widespread atrocities, but then again in the early stages the German submarines were very effective in sinking unarmed ships. They were very less effective in assisting survivors, and in the rules of war targeting civilians (merchant marine) and then refusing to render assistance to civilians (merchant marine) is, in fact, an atrocity.
So, yeah, the German Navy was out there killing people left and right using methods outside the normal usages of warfare.
The fact they didn't come back and machinegun any survivors floating around really shouldn't be held to be in their favor.
‘Scuse me. In at least one instance, a U-boat that sunk a liner/freighter, with lots of civilians on it, took the wounded aboard, tied lines to all the lifeboats, rendered aid, including water and food; began towing them, and called [in clear] his position to the Brits in [I believe] South Africa, explaining the situation. For his trouble, the British attempted to bomb him. He released the tow ropes and submerged.
As a result, Doenitz issued orders that the U-boats were not to engage in similar acts again.
Subs, of any service, typically did not hang about after sinking a ship. It would be a very stupid move, tactically. An interesting book to read is called “Iron Coffins”. It was written by a german national who started in the German navy in the submarine force as a middie, and through the war years advanced to skipper of his own boat. He was one of the 10% that survived. I recall a story in that book that involved a german sub on the surface moving towards a sinking merchie to render aid, and being strafed by an allied aircraft. The book is a good read.