I've always assumed that a lot of those messages are for historical immersion, to reproduce what was really going on politically at the outset of the war ("yes we're at war but we're hoping country X will change its mind so we don't want to make them TOO angry" etc.).
In terms of how the game keeps track of such things, once Germany is at war with a country, any ships flying that nation's flag are fair game. Even if you get a message saying "OMG don't sink British capital ships, we're hoping for a diplomatic resolution" it doesn't matter. The game doesn't keep track of that stuff when it comes to giving and taking away renown for ships sunk.
You should have a pull down chart in GWX with all the different nations' flags on it, it will have dates that tell you exactly when each nation "counts" as Allied (enemy), Axis (friendly) or neutral. It's really only the date and a nation's status on that date that matter, all other stuff about who can be attacked and who shouldn't be attacked because of this or that rule/treaty/gentleman's agreement/etc. can safely be ignored unless you want to follow those orders to the letter for the sake of more realism.
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