Balance wise there's absolutely no point to target subsystems in this game from practical point of view. Only if you roleplay or trying to disable target instead of killing it for mission or something.
When you just starting the game, and you fly small ship, your time-to-kill will be stupidly long, because in general game is heavily scewed towards engineering and medium-to-large ships for combat. You should really avoid combat early game in small ship with weak weapons and unengineered.
But if you absolutely have to, use smaller Beam or Burst lasers, depending how much your Distributor can handle, usually Beams are pretty heavy for it, and strap bigger class Multi-Cannons. Every Joe has to run this setup early game, because most other weapon combinations are irrelevant or downright weak. Also try to get used to Fixed mounts, so you won't have to worry about non-stop AI Chaff. Or if you can't, and still using Gimballs, when NPC fire off Chaff, untarget and keep shooting, it works like Fixed but with less damage.
If you target particular module, keep in mind: some are internal and some are external. Externals are usually easier to kill. To destroy Chaff launcher (which is really a waste of time), you have to physically see where it is located and shoot from that very side, targetted or not. Missiles are trash, never use them, because firstly, they can only damage external modules, so you won't be able to kill stuff like power-plant. And secondly, it would be a challenge to even destroy drives on most ships before you run out of ammo, because I've seen multiple NPCs having 3 Point Defences. None of your missiles will break through, while thier damage against shield is non-existent and hull one is absolutely laughable... Well, maybe against SLFs but that's it.
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