Here a few other answers from my POV.
1. Train in a different star system than your Capital. You will still face maintenance issues and overhaul requirements but if Fuel is an issue, that will save you some fuel.
2. Very, very rare. I have never have had a NPR appear from a closed warp point in my Capital system in the 8 years I have played this game.
3. Well covered by TMaekler.
4. Since the names are randomized, there is absolutely no link between the name of a civilian company and the ships they produce.
5. I do not subsidise my civilian companies as a matter of principle. However, the way I have achieved some level of control over the production of civilian liners is by preventing the movements of population by putting all my source colonies to 'stable' on the Civilians/Ind Status' Tab of the F2 page. Over time, the civilians will start to scrap their liners and not rebuild them, but that is admittedly a very slow process.
6. Already well answered.
7. The problem with the slow/beam ship approach is that an enemy crossing a jump point cannot fire, but he can move very well thank you. A slow/beam ship will quickly lose the ability to fire at this kind of target. You need to saturate the targets quickly and to me, that best done by railguns or missiles. Experiment with both and see what works for you.
8. Good points were already provided but all I would like to add is to chose your beam weapon early and then focus your research efforts. All the beam weapons have their pros and cons, it's a matter of experimenting and getting a feel for their differing capacities.
9. I do not know the answer to this.
10. I like to micromanage so to me, this aspect of the game is fine. In my current game, I have 9 Geo Teams surveying in 8 different star systems.
11. Unemployed Navy and Ground Force officers will also be released after 6 to 7 years of inactivity. The compulsory age of retirement is usually closer to 60-65 and that happens to all of them.