As far as I know they are just used to "harvest civilians", as in, blowing the Civ ships up and taking them as prisoners.
This will of course lower your rating with the Civ's in that sector.
The bounty hunters offer the possibility of specialized ships with over-sized weapon slots in relation to their sizes. If you want to avoid the bounty hunters altogether you can disable them during galaxy generation as they can be quite tough. If you still want the bounty hunters to be present but relatively harmless, then you can do the challenges they offer for respect, rez and specialists. Remember that if you are on friendly terms with them, they can occassionally enter engagements on your side when you go up against tough opponents.
For weapons I would recommend either beams or cannons together with missiles. You should get the desired category high enough so that you can use either the fusion beam or the particle cannon. Combine this with gravity missiles and if using beams, leech emitters to sap and slow your enemies to a complete halt. You can then order your ships to focus fire on the crippled target, tearing it apart quickly.
For armor, I would recommend you eventually maximize shields, armor and hull in that order because zombie critters will not break into your ships until you have a hole in the armor and missiles are the hardest to dodge and affect hull most, so having tough shields and armor helps most against those. Eventually you may also want to put some points into goons so that you can easier fight off zombie critters, boarders and repair the vessels faster.
Reactor and thrusters are also important. While the particle cannon and the missiles will not demand a lot from your reactor, the beams might. Fusion beams and leech emitters should be combined so that you can keep firing for a longer time. Faster ships will also last longer in firefights as they are not as prone to get hit as slower ships.
Avoid the use of more complex weaponry such as bombs, drones, mines, shuttles and stealth. You want all your ships to be as fast, heavy-hitting and durable as possible.
The ships you should attempt to obtain are ones that have mounts well suited for the type of weapons you have chosen. When I go Cannons I usually use turret-based ships so that I do not have to try and aim too much with the ships, while forward-mounts are generally good for beams which are easier to aim. Avoid the ships that use mines, drones and bombs. Bounty hunter ships are generally a bit better than UTA or CIV ships of the same hull size category.
Currently achievements are not affected by the use of mods. So if you do not mind then I would recommend that you get a mod that enables the use of more hangars. The game supports up to 8 hangars but the total number have been disabled due gameplay balancing and computer resource demands. Purists will not agree with this though.
You should always strive to outlevel the current star system you are in by at least 5 levels. If you are up against equal-level opponents or greater most of the time you are going to be defeated. Hard. Start each plot related quest with full levels of rez and goons so that you can rebuild your flotilla when your ships get destroyed. Between engagements always try to mine extra rez from friendly mining bases, and gather goons from battles where you are friendly with both the UTA and the CIVs. Buy lots of data using goons, buy goons using rez and mine rez from the friendly mining bases. Insane is a very unfair challenge and at times it can be a bit grindy. Hopefully this information will help.
Best Answer
I've played around a lot with missiles and I've found that they're quite weak when compared to cannons (cannons are definitely most powerful weapon type in the game).
The only success I've had with missiles is to put all my points into launchers and cloaking. Fill up all my available spots with torpedos (maybe 1 gravity missile). Put boosters in all none missile slots with the possible exception of drones, if you wish to pursue that tree. Get as many missile range/damage specialists as you can and then just barrage things from far away while holding the back button. If things get close, stop firing and run away.
If enough small ships or drones get in close enough, you'll have a very difficult time running away which can be problematic.
Against smaller ships, missiles are a better way to go as they rotate and track much better so you can constantly run away while firing, but they lack the power to punch through larger ships and stations, especially if they have point defense and/or zapper drones.
As for ship types, there's the volley for medium hulls, flora for large hulls, and carrier for huge hulls, though the star cruiser is alright as well.
If you are having trouble with zombies, try putting a laser into your turret and turn on turret auto firing. It works much better than PD for killing the zombie critters. Also, it helps if you never stop moving as you should be able to out run most of them. Zapper drones also target the critters.