I currently play the War Ace Campaign (WAC 5.01) which contains a lot of historical radio messages; I play it with the german voices and text. I don't know if all these messages are textually authentic, but I assume most of them are, taken from research and archieve documents.
On September 1-3 1939, when the war against Poland and soon after against England and France broke out, Admiral Raeder didn't issue an order like 'Sink them all', but he had issued orders citing the relevant international treaties of that time, and these were full of interpretation possibilities. At some point he issued an order like '...can be sunk if any possible threat against the submarine is noticed'. Some orders were even tragi-comic, e.g. when he issued the order (roughly translated) '...I want to ensure you understand that also ships from "Great Britain" are to be pursuied and destroyed...'
Such orders open for interpretation was very bad news for any neutral shipping at the start of hostilities, but latest in mid-1940 or late 1940 neutral ships like fishing boats knew very well that going off-coast was kind of a suicide, or at least they *should* have known, informed by their governement. Because german u-boat commanders had the same line of reasoning, fisherboats, or neutral boats with questionable flags (or without) and far outside of ports had to be considered as spies and were mainly destroyed, not because of tonnage consideration or issued orders, but as a precaution measure for not revealing ongoing operations and u-boat movements.
But was it really so? I don't know the whole picture, today all we have are interviews and archieves from the people involved and who made statements during and after the war. I would have to research myself.
A certain fact is, fisherboats and else, the naval sub war was a very cruel one, also in the Pacific battlefield. Sub commanders didn't ask many questions, they did shoot and asked later.