It's is definitely true that with bigger ships that tend to be slower and less manoeuvrable, the ability to manually target and attack subsystems is increased (and the likelihood of boiling them before you get malfunctions is less because they are almost always more structurally sound).
So on a slight (but related) tangent, it's always been our plan to have modules take longer to die completely, but suffer more malfunctions and importantly, suffer those malfunctions for greater periods of time.
The idea is that in a combat engagement, as a ship's shields are dropped, the chance of building up malfunctions increases. Not only do these malfunctions often provide the "advantage" an enemy might need to increase their chances of winning the encounter, they become a longer term challenge for the commander even after an encounter has ended, without being so permanent that they doom you to inevitable death.
However, in tandem with this, the actual effects of malfunctions will need to be toned down a little: for example, a malfunctioning cargo hatch might randomly eject a cargo canister every now and again, as opposed to spewing out lots in a single go.
I'd really like to get a "Millennium Falcon" vibe going, where your ship can be in a pretty battered state, still fully functional but prone to the odd "bang the panels" failure (or in Elite, the "reboot the module" failure).
Back on topic, whilst a slightly more randomised RPG-like approach still works, I'd like to inject the ability for players to "increase" their odds of attacking a specific subsystem (once they've installed the combat scanner that will be needed to view them, of course).
On another tangent, we're looking at various additional ways we can accommodate the pirate who wants to take cargo without killing their foe, as the changes we're discussing here would obviously have ramifications in this area as well.
When you have a ship targeted, you can look at the left side multi-function display and select the "subsystem" tab, then select the subsystem you want to attack (there are quicker ways to do this – you could, for example, set up hotkeys to cycle through a selected ship's subsystems).
When you have a subsystem targeted you should see a subtle hit marker on the target vessel. Lock on weapons (gimablled and turreted) will attempt to hit this marker, and you can manually aim at it.
Hits that are close enough have a chance to penetrate hull and attack the subsystem directly, once shields are down.
Note, damage that is transferred to a subsystem is not applied to the hull.
The location of the power-plant module varies from ship to ship, but generally the power plant is located directly behind the cockpit. I say this is the most important subsystem on a persons ship because if this module is destroyed, your ship will also be destroyed! It's an excellent module to target if your goal is to quickly execute your prey, for example, bounty hunting or taking part in the combat scenarios. This module is generally difficult to hit because it is usually located on the top or bottom of the ship meaning you have to be approaching from a very specific direction to get a direct shot.
This ship module controls how much power you give to systems, your engine or your weapons. Should the module be disabled, your weapons, engine and systems will be treated as though they have zero pips allocated! This will reduce your ship max speed, turning radius, increase the cool-down time of your guns, weaken and slow the recharge time of shields and reduce the effectiveness of your weapons. It's a major problem if this system goes down, but I honestly cannot think of a situation where you would want to prioritize this subsystem. At that point you're better off aiming for the Power Plant, since even with power distribution down, a ship can still be a threat. This module is often located on either the top or bottom of a ship to one side. It often mirrors the shield generator. If damaged, this system can malfunction and begin randomly assigning pips.
A fairly straight forward module that I'm sure you're all familiar with. If the cargo scoop is destroyed, you cannot deploy it any more and cargo will leak out of your cargo hold. A perfect module to snipe if you need to "liberate" a target of their worldly possessions without killing them. This module is usually located on the bottom of the ship, easily visible because it looks like two large doors.
Good damage percentages to know
At 60% health, a damage cargo scoop will dump roughly half your cargo.
At 40% health, roughly 90% of your cargo will have been ejected.
At 20%, 95% of your cargo will have been ejected.
Under 10%, most if not all, your cargo should be ejected.
Another module that you do not want to lose. Once your Life-Support subsystem goes down, your cabin no longer has oxygen and you start running on oxygen tanks. You have 10 minutes to get this repaired before suffocating to death! Either way, if this goes down, you want to head for the nearest station ASAP. This module is usually located wherever the cockpit of the vessel is or on the sides of the ship. It is important to note that the inside of stations are filled with air, so you only need to make it past the entrance of a station to be safe. If disabled, you need to repair it to about 80% with an repair module for atmosphere to return.
Another vital subsystem, this module is responsible for your shields. Should this go down, your shields will no-longer recharge. The location of this module usually mirrors the power distribution. Although important, it probably isn't a priority target in the heat of battle.
This module is responsible for steering and controlling your ship. Should this incredibly important subsystem go down, your max speed will reduce to about 10% of your max speed and your turning will be almost useless. Should this system go down, you are in a lot of trouble since you cannot maneuver or escape, but you can still frame-shift away assume that drive is still online. This module is located on the back of ships and is easily recognizable as a booster on either side of the ship. There are 2 drives on every ship, one for each engine, but if either goes down, they both are destroyed. An ideal target module if you're looking to incapacitate your prey without killing it. Fun fact: drivers produce the majority of a ships heat, so if you destroy a ships driver, often times they'll disappear off the radar until you get very close!
Another self-explanatory subsystem, this one is responsible for allowing your ship to super-cruise around. Should this go down, you lose the ability to super-cruise to different instances.
These vary widely from ship to ship: The sidewinder has 2 on top near the front, the eagle has 2 on the bottom and 1 on top, the cobra has 4 spread out, and these modules can be individually disabled if you aim for them. It often isn't worth specifically targeting modules like this, but it can be done. A disabled weapon/utility module can no longer be used. Shooting weapon hardpoints can occasionally cause them to fire and malfunction.
I call this a hidden subsystem. When shooting at a ship, you can aim for the windshield and break it. This will cause the HUD to disappear, and the oxygen to quickly leave the cabin of the ship having the same outcome as when the life-support module is disabled. When you go to a station to repair all subsystems, your windshield will also be repaired. If your goal is to break the opponents life support, it may be easier to aim for the windshield to get the same result. The only drawback is that you cannot tell when you have broken their windshield since there is no visual indicator.
Durability
Different subsystems have different durabilities and some are harder to hit than others due to location. By shooting a module, you can do partial damage depending on whether its a direct hit or not. As for how much it takes to kill a subsystem, it's hard to say. Bigger ships seem to have more resistant subsystems, and a single railgun can destroy a subsystem on everything up to a cobra, and it takes 2-3 to destroy a subsystem on an Anaconda. It takes roughly 20-30 shots with a class 2 pulse laser to disable a subsystem on a cobra. Slightly fewer for a sidewinder or eagle. Life support seems to be very fragile, drives are pretty tough, and cargo bays are somewhere in the middle. More testing is needed for the exact durability of each subsystem.
Side-sensitive
When you target a subsystem, a reticule appears to help show you where the system is, but most subsystems can only be hit from a certain side of a ship. For example, you cannot shoot the cargo scoop when you are above a sidewinder, you must be below it. This goes for most-if not all subsystems.
The AFM Module
This subsystem goes in the support slot of any ship. What this module allows you to do is repair an offline module over time via the module's panel on the right side of the cockpit. It repairs at 1-2% per second (so, relatively quickly), and is great for when your far away from a station and something critical like your life support goes down. There are some drawbacks though. To repair a module, it must be offline. You cannot repair the Power Plant.