From many of my readings, it was very historically correct that u-boats would engage most unescorted or lone merchants with a warning shot. In some cases this would inform the ship to abandon to life boats prior to attacking. This method would have been more appropriate at the early war years, and it aided the u-boat captain in making proper ship I.D., while noting patterns of cargo types and routing, etc.
As things quickly progressed on both ends, the u-boat surely needed quick kills to get in and out, as well as to limit merchant distress/sub reports to HQ, and merchants armed up their decks and needed to keep the cargo moving.
I like the fact that you are trying the warnng shots over the bow (or bettter yet, into the bow),
yet in SH3 simulation, just "get in there and get er' done"!
