I try not to let these issues worry me. I enjoy SH3 immensely, regardless of the accuracy of history.
If you follow SOP, as laid down in the U-Boat Commander's Handbook, the target in your sights is worth more than the huge merchant you have yet to find. Kaleuns that held off from engaging a target because it was too small to be considered a worthy addition to their tonnage score usually would find themselves in a world of trouble from BdU.
Donitz wanted his commanders to be like aggressive attack dogs.
Sink 'em all!