I just responded in SE4C forums to this, but I guess I can post it here to if it's any help
1)It only increases Planet conditions, and thus raising the reproduction rate, and maybe happiness. I havn't been using them to much. You can scrap them when it's done. Infact, you'll get a message in you're log that you cannot improve planet conditions anymore.
2)Depends on what you want the mines to do. If you want them to stop ships from entering the system you just load up on a ship with minelayer components and move it to a warphole. If you want them to act as planetary defense, but 'em in orbit before combat, since PDC will easily take them out if you launch them in combat.
3)If you give the ship orders to move to "Resupply Planet I" in the "Test Sytem" and on the same turn, before it moves there, you can order it to go to the planet "The tester" in system "Elinga" the orders will stack in a queue and will b completed in the order they where given.
4)By increasing size, the direct fire weapons can also increase firepower. But you can't select certain mounts if the ship is too small.
5)Any unit (mines, fighters, satellites, troops) can't be retrofitted at all. Ships however can as long as they are in a sector with a spaceyard. Now, old destroyer class with shields lvl II. I wnat to upgrade the destroyer to have lvl III. I click upgrade and name it something like "Destroyer Mk II" (Mk, stand for Mark, meaning something like Version 2)Then I retrofit my destroyers to this new design.
Note: You cannot make the destroyers to be cruisers, you are only allowed to retrofit beetween designs, not hull sizes.
6)If you see a system that you have no ships in (For example if you start with the trait "Ancient Race") and an enemy already has colonized the planet, but you can't see his colony because you have no precense in there.