One way you can do it is by editing your main.cfg where you have Time Compression (should see this section when you open it in notepad) located in:
C:\Users\username\Documents\SH5\data\cfg
Look for Enemy Detected=1 and make it =8 or =16 or whatever.
However, this will be the default for every time an enemy is detected which could see you fatally damaged before you realize they are there so I'd suggest that when travelling you turn on the option at the top right of the GUI named TCx1 on any message box. Of course this could cause even more frustration if you are in shallow waters for example so it might be best to just live with the sighting messages as they are I'm afraid. There may be an option in TDW's OptionsFileEditor but if it made things better without serious other compromises I'm sure it'd already be default.
Unfortunately, issues like these are something we subsimmers have to live with and you sometimes just have to try to ignore it. Just consider it an over-enthusiastic Bernard trying to prove himself as a capable watchman.
As far as the mission completion goes, all missions are now date based in WoS, there are no progress bars at all, so you're free to do as you wish without penalty, bar sinking friendlies or neutrals. I'm sure someone can give you some firm dates on progression and when new missions will appear, but in the meantime, just concentrate on cutting off those essential supplies.