Jeff:
To summarize the above and answer all your inital questions:
1. Like the tech tree, the different SB module "paths" are color-coded. They are linked to the tech tree...if you research a Comm tech that allows new SB modules, those SB improvements will appear in the yellow section marked "Economy". Over time, you will learn which fields to research based on which color of module you wish to improve your SB's with.
2. The game does allow you to build modules that have no current effect, either in your present game (no planets in sector), or the current build of GalCiv (a rumored expansion capability is that you will be able to research star/planet creation techs to make your own inhabitable systems).
When the description states a module will help production on nearby planets, it means that any colonized star in that Sector will benefit by the increase specified. (You can read the cumulative production bonus for any planet on its "Details" screen after double-clicking on it in the Star menu.) If there are no colonized planets in that sector, the bonus is ineffectual. This is true even if a colony is 1 parsec away, over the sector "border" (line) - the bonus is sector by sector, with only influence extending into adjacent sectors.
Ships bonuses are calculated accrding to the sector they first start their turn in. These bonuses stay throughout the turn and will apply even if the ship leaves the sector. However, on the next turn, bonuses will be re-calculated based on the new sector the ship is in. For this reason, it is sometimes worthwhile to build a SB in an unoccupied Sector which is strategically important to your Fleet, putting Stellar Wakes and Defensive modules on it.
3. The arrow next to the module is a drop-down menu which list subordinate modules you have completed (much like the collapsing file structure in Windows Explorer). In this way, you can see which modules are prerequisites of other, higher-level ones.
4. When mining a resource, your inital SB build gives you a 5% bonus Empire-wide in that resource. Subsequent Mining modules will increase this bonus by the % stated. The lesser-amount % modules are frequently prerequisites of higher-level modules (which means there is always a reason to build a 3% module, even if there are 5% & 8% ones available at the same time...eventually you will research a tech that gives an even greater bonus, or a brand-new capability, and it will require one of the 3% modules to construct).
5. This is all derived from experience. None of the above is documented in the manual.
~SDC~