These missions are usually fairly easy as long as you know what you are doing and its not someone inside a military building or a... i forget the word, but basically a target who has their shields up. Can't remember whether its because they are a super soldier or because they know they are being targetted. It basically tells you in the mission description to expect a hard target though.
Check out StealthBoy on YouTube, he has a guide for this sort of thing.
Regardless, a tormenter to the head (with silencer mods) or use of the zapper ensures you can get away cleanly without raising alarms, with some caveats.
1) The aforementioned target with shields up. I've only had these outside, so usually not a big issue, but they can't be taken out with the zapper and require a few shots. Get close to them with your silenced tormentor and quickly take them down when there is nobody else in the area (just so they don't spot it happening or find the body before you get out of there).
2) The absoloute worst variant, where they are in a security building, often in the same room with another NPC or there is one wandering back and forth. Sometimes you just have to kill multiple NPCs quickly to avoid raising the alarm. Plus getting into the building without being detected can be a pain. Do ensure you have remove fake security clearance bound to a button to get rid if you are at risk of being scanned somewhere you can afford to drop the clearance. If you are going to get scanned somewhere you shouldn't be, you're going to have to take someone out.
3) Missions that state you can't raise the alarms leaves little room for error, although it mainly just means making sure the body isn't going to be found before you get out of the instance. For those missions though, the target can usually be taken down in a location where they won't be found. You can go to the effort of disabling the alarms, but that to my mind just increases the risk and duration of the mission. Perhaps i might consider it if the target is in a military building, where i'm going in anyway. Oh yeah, it really helps if you know the layouts of security buildings really really well.
4) Don't kill anyone but the target missions. These i don't like, because it really constrains you if things go south. Once practiced, you can usually do them without a hitch, but definitely to be avoided until you have mastered assassinations in general. If you find someone starts shooting, best option is just leg it to the target, kill them, then run for it, without killing anyone else, or just leave the base and return later to complete it (after clearing any wanted status).
Just in case things do go south, its always a good idea to have a very heavily shielded ship, as you're going to be legging it to the ship, which will come under fire, and you have to transition to the ship and take off, all while under fire. You could go in via SRV, but those things will blow quickly if targetted after the base is alerted. I generally advise a small ship (land anywhere, especially close to building where the target is, or on any pad) loaded with shield utility slot shield boosters and guardian shield boosters. The iCourier, CM4, and Vulture are good choices here.
Like with everything practice makes perfect. Watch some guides, then give it a go.
