1) Faction raids : I have 3 colonies in a star system east of the core worlds, and i'm having good income (approx. 300k a month). However, the factions, some of them having very good standing (50+ reput.) with keep attacking me, sometimes 2 of them at a time. It's not a real bother, but i don't really have good defenses up yet, but each time i kill them i get -5 reput., and i can't farm story points fast enough to bride everyone. What are you supposed to do about that ? If your faction reboots them without you attacking those faction fleet, do you still eat -5 reputation ?
You get -5 rep if the expedition fails, no matter the cause, I believe. As in that raid fleet can encounter and die to a random pirate fleet in hyperspace and you'll still get -5 rep.
As for what you're supposed to do about it, realistically, wait for the next update. There's supposed to be a cooldown on these sorts of expeditions so that you can only get 2 per cycle at absolute most, but it doesn't work.
2) Military bases and colony size : alright so i only have fast pickets because i didn't know you were supposed to build a military base. However, i'm seeing on the wiki that the quality and number of fleets you get depends on the size of the colony. However, my main colony is an income colony, that has heavy industry but no military base : the military base is being build on a forge world with higher hazard rating. My questions are : does the colony keep growing after 6 where you get the maximum industries but can't pay hazard pay anymore to stimulate growth ? If that's the case, is the max size attainable with high hazard colonies (meaning you're supposed to implement your military base on a low hazard colony ? Also, does it matter that the colony that has the military base isn't the one that has the heavy industry (for ship quality ?) ? Also also, therefore would you say you NEED to build a military base on every colony ?
Player colonies are capped at 6 regardless, unless you change that cap in settings.json. Colonies visibly "growing" past that point is...not sure if "bug" is the right word, but it's attention to detail that was missed.
Military bases and heavy industry are separate. There's no special benefit to (not) combining them on any given planet.
I don't know about "need", but it is something you can choose to do. Military bases (or High Commands) don't generate income from exports and are fairly expensive buildings to maintain, but they do increase security and stability beyond what a patrol HQ does. It's up to you to decide whether a particular colony (or system) needs it.
3) Capital ships quality : alright now that's something i just noticed and was baffled about. I recovered 2 Astral capital ships in my travels, and kept them in storage. Now i have the cash to restore them (3 D mods on each one of them). However, one of them has 27 max speed and 0.66 flux per damage on shields, whereas the other has 30 max speed / 0.61 flux/shield : and it's not a D mod doing that. Are there randomized quality stats for capital ships ? How do they work ? I compared, other common ships like mules have the same stats on the hull unless they have D-mods, but I have 3 conquest and one of them has slightly better speed/flux per damage stat. Also, the Astral top speed, on both the 27 and the 30 speed one appear in red, that means it's lowered by something right ? However the wiki says the normal max speed is 30 so i don't get it...
What you're seeing is the result of Combat Readiness. If a ship has low CR (I think around 40-50%?) they start to take penalties to various stats, including top speed, and beyond that they will start to suffer from malfunction chances (30%) and eventually critical malfunctions chances (10-15%, I forget exactly). Conversely, if CR is raised above the default limit of 70% a ship will receive bonuses to it's stats. All you need to do is repair your ships using supplies, either over time or at a dockyard, and the low CR will be fixed.
Note that you might need to hire more crew - like,
a lot more crew - if you're taking capitals out of storage like that. All ships have a minimum crew requirement, and being under that penalizes your fleet's CR caps. Capitals need lots of crew, so if you're taking big ships out of storage you might need to prepare enough crew beforehand (or just keep extra crew in storage along with the ships).