4. The advantage of deploying small mines is that the mine sweeper components sweep a fixed number of mines--small, medium or large. For the same cost, you could deploy twice as many small mines as medium ones, and they would be less likely to be sweeped.
It is possible that large mines have an advantage when attacking the ship. I can't remember if the consensus is that mines attack the ship one at a time or warheads. If it were mines, then someone thought a large mine might penetrate your armor while a small one wouldn't. (I think they said that if the first mine didn't penetrate the armor, then none of them would?) However, I think the Last commentary I read thought each warhead attacked the ship. Hopefully someone wiser than me will post the answer.
5. Intelligence - I don't think anyone has quite figured out intelligence.
We do know that a level 3 CI project will run longer because it has a higher cost. But other than that... lots of theories.
6. I think remote mining is a *huge* waste of resources. You are much better off building a colony ship and colonizing the planet. If you can't colonize it now, you'll eventually be able to colonize it. It has to be a very good planet (probably with moons) to be cost effective for very long.
8. Exactly. Without multiplexing, your ship might have 20 weapons. If the first weapon kills an enemy ship, then other 19 won't fire until the next combat turn. But with the multiplexer, you can fire at multiple ships.
10. Ripper beams lead to the Wave Motion Gun. That's about their only purpose.
Some folks really like the shield recharger components. If you fight pretty even battles in terms of numbers of ships and technology, maybe they are okay. I don't use them since I just play against the computer and always have superior numbers. Maybe in PBEM/PBW they are very effective.
11. Right. You can put as many Repair Bay III's as will fit on a ship, and all of the Repair Bay III's will repair components each turn.
12. Phased shield stop all damage. BTW, at one time there was a bug in the game that disabled the 'phased' effectiveness of phased shields if you also had a normal shield in the mix.
Hope that helps. Have you downloaded any of the shipsets available over in the Mod Forum?