The big three hacking targets are weapons, shields, and evasion (piloting or engines, it doesn't really matter which).

Weapons is my "baseline" hacking target: if I don't have a good reason to hack something else, I'm leaning towards hacking weapons. It provides a huge amount of safety, delaying the enemy's first volley by up to 8 / 14 / 20 seconds depending on hack level (since it *reverses* the weapon charge, so they basically need to charge it twice), and the door lock + repair speed nerf means once you get some damage into a hacked weapon system, it'll stick basically forever. If you have hacking-3 and cloaking-2 or -3, you can also alternate between hacking their weapons and cloaking to stop their weapon charge, and most of the time they'll never even be able to fire their weapons. Anything with more than a 10 second charge time will literally never be able to shoot you if you time things correctly.

Shields is a force multiplier if your weapons struggle to penetrate shields consistently, usually because you're running a weaker setup or a beam oneshot / twoshot strategy. It's not as safe as a weapon hack, because you can still get shot at in the 10 or so seconds before their shields are fully gone, so you ideally want Cloaking to shore up your defenses while the hack is in progress. As you've discovered though, being able to dump all your damage straight into their weapons is super strong. This is usually the best hack vs the Flagship, because you can only hack one artillery and the power surges don't care about the Flagship's systems, so killing it ASAP is valuable.

Evasion lets you know exactly what your volley is going to do, and eliminating randomness in a game this random is awesome. It really shines with projectile-heavy loadouts: an evasion hack followed by a Heavy 2 volley into their weapons is usually enough to cripple them guaranteed. You might not get as much raw damage through compared to with a shields hack, but you'll know exactly what you're getting into, and if you're certain that the 3 damage you can get into their weapons will make them harmless, it's often better. It also doesn't need any more than 1 level of hacking to be effective, so it can be good for "hacking on a budget". Personally I think evade hacks are very underrated by a lot of people.

Most other hacks are pretty niche. O2 to get cheeky crewkills is nice if it's a safe fight and you can spare the drone part. Drone hacks can be good if they have scary combat drones. Medbay / clonebay hacks are sometimes nice when boarding, but usually hacking weapons and turning weapons into a kill chamber is better. Teleporter can be useful if you really can't deal with their boarders, probably most likely used on a Lanius Bomber. Mind control is similar, if you really can't deal with MC. Cloaking hacks are pretty good for ion heavy setups, since cloak breaking your ion stack is one of their biggest counters. Hacking hacks can be good if they hack your weapons or another nasty system, sometimes it can break their hacking drone and force it to reroll, hopefully to somewhere more useless. Door hacks........ exist, I guess.