I'm at the point where every mission now has enemies with 180 aimbot hackers that not only see you from across the map at night, but instantly noscope headshot your camo'd girls behind cover, when shot in the back.
Sounds like you've met the mercenary faction or even the Star Gods! Thankfully most of the enemies in game are much less capable of such things.
Does splashing civvia ships definetly give negative points?
I don't think so. I think you stand to
gain points as long as non lethal force is used on the civilians.
So looting civilian ships for engines and captives is the main way to make money?
Looting shipping, including civilian craft, is a good way to make money. You're a pirate.
I just got eurosyndicate and they sold me 8 laser rifles for 4M. This should deal with those armorued enemies effectively right? What armour should I be trying to get?
Those lasers will deal with a lot of armoured enemies very well. Others, not so much. I'm not going to tell you which weapons work well against which faction; that's for you to discover (It's probably already discovered in your bootypedia). I can't tell you what armour you should get because they can all be really effective with the right equipment. What I can tell you is that by year 1.5 I like to have everyone wearing guardian armour because I prefer the massive armour values and resistances it provides. My armour progression starts with warrior and camo paint, then progress to tac armour (with the helmet), then to defender, then to guardian.