Hi and welcome.
From an overall point of view I would advise you to buy the game. It is available at low price, even with addon, and the change of scenario (including using the U.S. yard system and stuff like this) together with the fine graphics give a whole new and exciting experience. I felt this even though I left behind a wonderful SH3+GWX3+SH3Com installation also (as I don't have time to play both). And I don't regret the buy.
Now to your specific questions:
- No weapons officer, but can use active sonar for range estimations as long as no warships are around. This makes it easier. You should be prepared to go fully manual on targeting or use the auto targeting option. But this would also just simulate your weapons officer doing the work, so I don't see the real difference there.
- There are very well received 'all around mods' available. Check out the stickies in the mods forum. Real Fleet Boat and Trigger Maru are the most heavy used ones there while the Pacific Enviroment or Real Enviroment turn onto some nice graphical changes and the 'Run Silent Run Deep' Campaign is a nice improvement over the stock version.
The only thing I'm missing is the OLC GUI for SH3 which built in a cool range/AoB finder into the game. I don't know if that concerns you as you said you avoid full manual targeting.
- This TC issue I once had with destroyers in a highly moon lit night. They saw and attacked me before TC could bring me back onto the brigde to give orders. There is however a built-in solution for this: the first time your crew spots some contact (e.g. warship) it will jump out of TC and provide you with a short dialog what the default option on such an event should be. So you can (don't have to) set that for example you want to dive to periscope depth every time your crew spots a warship on the surface. That might get rid of this issue but I didn't try it yet as I left this option always on 'go on with current orders'.
- Addon is not really necessary but the new career might be a nice change as well when you feel you've played enough fleet boats. It includes the 1.5 patch but I didn't check the change list of this patch yet. As far as I know, the super mods as well as other big ones are also available as a 1.4 (pre-patch / no-addon) version. Better check this again in the mods forum, but you can hardly go wrong either way I think.
Jut consider this: The addon adds no content to the fleet boat scenario, only the U-Boats in the far east as a campaign on its own (including IX/D2, XXI and XVIII boats). Buying the game and addon as a bundle might just save you some money over buying SH4 alone now and the addon later. Mod-wise you might just be on the safer side getting the addon but I've also seen good support for SH4 1.4 in the mods forum also.
Have fun playing