NP!
3) Eeeerm lemme see: changes of that nature would be controlled by the CSV merge/load order which I actually have no idea what the rule is (been a long time since I've needed to mess with it). Anyone reading who remembers how csv merging of duplicate entries works?
4) If there's a real memory leak than increasing memory will only delay the problem and the game will still get unstable after a certain length of time. For just massive numbers of mods that take system memory but don't have leaks, increasing the memory will let you run more of them. A bigger problem with many many mods is video card memory: more mods means more graphics means more loaded sprites which can take up a surprising amount of video memory, especially with graphicslib and normal mapping. Exceeding it will give a large performance cost and there really isn't anything to be done about it.
For in combat performance, more entities will tax the CPU and bring frames down, and more mods will do the same as many mods are using scripts that loop over enemies/compare in an O(n^2) fashion. Even without more entities some mods will impose small performance losses due to just doing checks etc for their gameplay during combat, but in general authors are aware and keep things tight. Mods like Lazylib/magiclib etc are really good to use because the authors put work into doing implementations that are not performance hogs.
One pitfall I forgot to mention earlier: engines are surprisingly performance intensive. If you are making a faction that spams little fighters/drones, giving them more than 1 engine can tax weaker systems (and even in the base game I wish the fighters would get less engines).
The game lowers framerate but keeps the "speed" of combat the same until it hits 30 FPS. Then as framerate slows the game slows down too (so a game playing at 15 FPS is going at half speed).
The game does not simulate all entities everywhere - a lot of things get 'packed up' when the player is not around. I think everything in the system the player is currently in is simulated. This is a potential modding pitfall as there are ways of adding things that don't get packed up, I think? Not entirely sure. Things like hunter fleets chasing the player and expedition fleets are simulated travelling through hyperspace I think (again if someone knows better please correct).
6) I believe beams have their damage applied every 1/10th of a second vs the armor's current value, using a 'damage' of 1/10th the DPS but a 'damage for the purposes of armor reduction' of 1/2 DPS (this would be the DPStoHit it seems). The formula for damage reduction fraction is (damage for purposes of armor reduction)/((damage for purposes of armor reduction) + (armor value with modifiers)), which is then multiplied by the damage being dealt. (There are some threads about armor mechanics and I believe the wiki is up to date:
https://starsector.fandom.com/wiki/Armor