1) It depends. If you play with Organic, you'll need organics for all the weaponry and armor. Certain components (notably Master Computers) and facilities (like the shrines IIRC, and Atmosphere Converters) also cost a LOT of each resource.
So it depends on what tech you have, and your playing style; if you use entirely conventional foo (crewed ships with standard weapons) the rest won't be terribly important.
2) Select a planet. Click the 'Abilities' tab. If the planet has a high population, you should see a bonus to production because of it; if memory serves, it goes up to +80% or so in 0.99.
3) Never played SE3. But my suspicion is that it's buried in a text file, and in the full Version if you care to change it, you can.
Keep in mind that mines are cheap. Mine your warp points and you'll need fewer ships to defend a system (keep a small fleet within range of the warp points if you think they can breach the minefields).
4) Yeah, it'd be nifty.
5) Haven't bothered yet.
6) Hrrrrm, can of wyrms; it'd require allowing components to remain in planetary inventories, and that seems a tad problematic in terms of added MM (getting rid of old stuff to free space). I'm fine for now with the excuse that yanking weapons and armor off a ship is hard to do non-destructively.
7) For now, they're robots. =)
8) One could assign a probability of failure instead of out-and-out damage, as well -- *may* fail when used, may not, so as to leave the player guessing. Takes additional coding, however (more state to store).
9) Aigh. For now, hit spaceports. I find that turning major colonies into ashes is disruptive enough, for now.
10) Play without spaceports, and I think that might be what happens. ;-)
-- The thing that goes bump in the night