I haven’t found any info on routine German Navy atrocities. Do you have any info?
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.