As for whether or not the shield modules decrease the damage of weapons, I couldn't tell you. As for module load-out, though, I tend to agree with Bognor - but with the caveat that it depends on what you want to use the modular fort for.
Ran out of forcefields but want to put a shield over the (non-military) command station while still leaving the fort able to contribute to wave defense on the wormhole? Missile turrets, or anything else with a really long range, unless you're comfortable placing the command station close to the wormhole.
Centerpiece of a heavy defense grid designed to stop waves, CPAs, etc, at the wormwhole? Either a balanced module selection, or a selection that compensates for whatever happens to be lacking in your defensive grid.
Only defense of a planet? Balanced module selection, or whatever happens to have bonuses against most of the AI ships (if only one or two modules cover that, anyways). Alternatively, all missile modules (or other very long range weapons), assuming you just want to deal with minor threats or cause some slight damage to AI vessels passing through or raiding, or want to keep the fort out of the way of something like an Astro Train (if they still shoot, anyways - I haven't tried a game with them since the Astro Train revision).
Against any sort of mixed attack (raid engine, CPA, exo-wave, whatever), variety should trump mark level.
This depends heavily on what the other defenses on the planet look like and what the AIs are using. If the planetary defenses were relatively balanced before adding the modular fortress, then a balanced module selection is good first guess for module selection. If, on the other hand, the defenses are unbalanced, then it can be a good idea to use the modular fort to balance things out (for instance, if I only put sniper and missile turrets on a planet and now for some reason want to fortify it without adding additional turrets, choosing weapons for the module slot that have bonuses against things not covered by missile and sniper turrets may be good - unless the goal is to sit at long range and whittle down the enemy without taking fire, as at a grav drill). Also, if the AI forces lean heavily towards one hull type, or a hull type countered by the same weapon module, it's probably a good bet to prioritize getting more weapons that have bonuses against that hull type rather than having a balanced selection of weapons on the fort. In particular, if something like fighters are the only thing that the AI has that a particular weapon is good against, you probably don't want to spend module slots on that type of weapon and should prefer a weapon that performs well against a more dangerous AI vessel (like bombers or raid starships).
