Questions:
-Is it possible to lock shields in a side position?
-Is it possible to have shields take higher/lower damage in different places?
-Is it possible to have different armour strengths on different parts of the ship?
-Can you have it so that only certain weapon roles can be mounted in certain spots? (e.g. a close support only slot)
- I don't have the API handy, but I'm fairly sure you can. Problem is, the AI won't understand it and it might not have the effect you want.
- Easily, but like the previous one, the AI won't "know" how to use it to it's advantage. Might be okay, or it might not. Depends a lot on the weapon layout to "trick" the AI in the behavior you want.
-Technically that sould be doable: you can have a global high value for the armor and damage some cells at the start of the battle, then and restore them at the end. However it's
very involved, and while the AI will be able to understant it, it won't apply to auto-resolve or AI vs AI battles.
-You can easily do that, but you won't be able to make a custom UI to explain it to the player.
Overal my main concern would be what purpose will that faction fill? What I mean is that those ships doesn't seems be great additions to a player fleet, their main attribute being burn speed at the expense of everything else. But burn speed is a finicky attribute, +1 burn compared to vanilla is a small edge, +2 is overpowered as hell since Capships can then catch slow frigates! So there is not much room to play with that.
And the player won't have much interest in attacking them if they are pacifists: It's closer to be a civilian independent faction. So while interesting for the universe's flavor, a mod like that is still is an awful lot of work for little return.
Don't get me wrong, I really like the underlying idea (I'm even making Seeker for similar reasons), but I think you may need to refine their goals and purpose from a campaign gameplay perspective before comiting yourself to the wonderful but exhausting world of modding. Otherwise it could lead to a lot of frustration after a lot of effort...