Hello again, Peter.
I hope my limited experience with the sim can be of some help again.
1. I've only seen the message appear a couple of times in the vanilla (i.e., non-GWX) version of the game. Sometimes it has been something like "Your flotilla has been transferred to Bergen." When I get messages that look similar to yours, I go to the F5 map and either drag it to the port shown, or I zoom out so I can see more of the earth, and just look to see in what color the port's name is printed. If it's blue, it's under Axis control; green means neutral, and red is Allied. When I've run low on fuel from missions that are 12,000 km in a boat with a 6,700 km range, I've put in at friendly ports to resupply (I have to "end" the patrol there) and can get a full load of fuel and get more torps there. If I recall correctly (it's been awhile), medals and promotions earned up until then will not be offered until you return to your home port, or the one to which your flotilla has been moved.
2. It's possible that you're confusing "missions" with "careers". The missions (again in SH3 1.4b, not GWX that I know of) have you start in a a specific location with a specific object to achieve, like defending your remaining surface fleet in northern Russia, or sinking a couple of aircraft carriers in a moving task force, etc. In Scapa Flow, you're to penetrate the defenses and make it in to sink the Royal Oak. Patrols, as far as I know, only appear under "Careers". Each time you make it back to your port alive, you're assigned a new grid to patrol for 24 hours, which of course means you have to get there alive, complete the patrol, and get back alive (or "warp" back, if you don't think you'll make it).
3. I you enable "external view" (or "external camera"?) in the Options list, you can hit the "," or "." keys to see yourself and any surface ships that have been detected -- also aircraft sometimes. It won't give the name of a ship; you'll still need the recognition manual accessible from the periscope or UZO view unless it's a ship you can identify easily. I have GWX on my less-capable laptop, and while the periscope view is better, it's still pretty frantic to page through the recognition manual as *something* is bearing down on you at 22 knots from 3 km out....

4. I've seen a Bogue-class carrier at Firth of Clyde, and a troop ship at Plymouth, I think it was. There was a large cruiser one time when I sneaked into Reykjavik after finishing my assigned patrol area just south of Iceland. The big prizes often hide at the "rear" of the docks, beyond the easier C2 and T2s that are easily spotted. Warning: I found that, even after being holed enough to settle on the bottom (about 7 meters) while dockside, the Bogue keeps its guns manned, and they can still shoot at you if you surface on the other side of a pier to shoot at the tanker at Firth of Clyde.
5. If those are mines, I've been exceedingly lucky, as I've run into lots of nets. However, if they *are* mines, they're so close to the surface that only very shallow draft vessels would be able to clear them, so perhaps they are defense against substantial enemy surface ships not using the channel that's designed by the port's "owners". So I don't know, but the nets can sure do a lot of damage to the bows of your sub, like the forward torpedo, forward enlisted quarters, and radio room. I've learned to keep a full Damage Control team on duty when entering enemy ports, it sure speeds up fixing those "Oh, geez!" maneuvers. I've also tried using the observation periscope raised until it's just clear of its housing, but not above the water's surface, to have a chance of seeing the nets *before* I impact them.
6. I don't know what the stock limits are for deck/flak gun weather states, so I've cheated somewhat by putting in the "any-weather guns" mod. It's completely unrealistic, as the deck gun frequently spends as much time underwater as above, but when I'm lazy and playing in Arcade mode instead of "realistic", it's all about tonnage and airplane kills. (A couple of tweaks to the supercharger factors, and I've got a Type IX-D that will do 66 knots on the surface, but 5 knots at the slow setting, so I can navigate in ports.) Some of the more seasoned Kaleuns here will doubtless have more definitive weather values to answer this question for you.
7. Aside from the area directly south of Ireland, and west of Gibraltar, I can only find good hunting grounds by using the map showing naval, convoy, and air protection areas. The map is in the program under "Documentation", along with 4 or 5 other handy docs. I leave the map open on my desktop under the sim window so I can Alt-Tab to it every so often. As soon as I win the Irish Sweepstakes, or get the money from the nice gentleman at the National Bank of Nigeria, I'll have that map printed out in 17" x 22" and laminated so I can hang it on my wall, mark it with a grease pencil, and erase it with a wipe after each patrol. FWIW, my two adjacent walls have maps from Eve Online, and amateur radio country designators and a pin map for contacts in those countries, counties in the US, etc. I'm not a multi-tasker, but I've got lots of interests

Hope that helps a little, but you'll undoubtedly get more informed answers from the more senior members here.
Toodles,
-- Zygoma -- kl7hny