Agrajag,
I have never seen what you have described about ports not showing up.
For 1st flotilla, Wilhelmshaven is available to about July-1940, and Brest should become active in August-1940. Even if Brest doesn't show up at the end you your patrol, I'd still head to the Brest area (see pic below, it's a bit east of grid BF-28 and BF-52) and 'end patrol, dock at Brest'.
If you can't 'dock' there, just 'end patrol' and things should be docked at Brest for the next patrol.
The 'Null' patrol area is a game bug. Pressing the F8 key should still display your patrol-area, but I don't think a player gets renown-points for patrolling a Null area for 24 hours. The Null bug usually shows up about 1 or 2 times per campaign.
For fixing your sub and loading torpedoes, make sure 'silent-running' is not engaged. Press the Z-key to 'secure from silent running'. Then repairs and torpedoes should work if you have repair and torpedo areas manned.
You will see bigger merchant ships as the campaign progresses. Especially late 1941 and onwards.