From what I know: The most important messages for your gameplay that reveal course and timeline for enemy convoys or formations or wether you've been detected appear in the Captain's Log at *any time* and AFAIK with 'Easy Contacts' set in the Options: it stops time compression so you are warned. You will see a new grey Contact Mark on the map if you play without Real Navigation, however this information may be only approximate, thus not precise at all.
With Real Navigation I expect (but I don't know) these new contacts to have NO warning, it's your business to check the Captain's Log, so you better look there often or you miss opportunities
Thanksfully the Captain's Log is saved when you quit your session and saving the game. And that's very good because the 'message' section is NOT saved unless you save it together with the supermarks which is only possible with mods like TWoS.