It's not as hard as it seems to stealth kill, but it does take some preparation as enemies get stronger. First thing's first, put some points into Cool and unlock Silent and Deadly to get a nice 25% bonus damage to silent weapons while sneaking. Crouching Tiger can be handy too. If doing a lot of stealth I'd also Recommend Hidden Dragon, especially for missions when you're supposed to take enemies alive, but even if you don't want to you can always execute them after you knock them out.
If you want to kill without grabbing them I definitely recommend handguns over rifles. You need high damage per shot, not high DPS, and the ability to attach a silencer. So far the best guns I've found for this role are DR5 Nova, Tamayura, and Overture. If you're learning crafting you can make your own DR5 Nova pretty early on.
From there you want perks, mods, and cyberware that increase handgun damage, headshot damage, crit chance, and crit damage. I won't attempt to list everything that can do that, there are ways of increasing those things all over the place and they all stack. It's actually super OP. Eventually you'll get to 100% crit chance and be popping heads for massive amounts of damage. If you prefer melee it might be a little tougher, but there are similar ways of increasing relevant melee damage and crit stats. Also keep in mind that when you make a melee attack you will stand before you swing, so aim low. A little practice and you'll be taking heads off.
Another bit of advice. Be ready to quickly follow up if your first shot doesn't immediately kill the enemy. If you're against tougher enemies or haven't got good enough equipment and perks your first hit might not kill. This will alert the enemy you just hit, but you have a few moments before they warn their friends and if you finish them off quickly enough it may not alert them. This depends on proximity, though. If they are really close to friends they're going to go into alert even if you 1 hit. I think what's happening is they are alerting on the sound of the corpse collapsing. This is why you can choke someone out right next to them with no alert at all. If they are far enough apart they won't alert from the corpse collapse so you can use any silent weapon as long as you aren't seen.
Hacking is your best friend as well and can greatly enhance stealth. Using devices to distract enemies is good, and also a great way to apply a breach protocol to them so you can hack the enemies themselves for cheaper ram costs or to apply Mass Vulnerability to weaken them. Ping is great for revealing enemy positions and threats you haven't seen. Sonic Shock and Reboot Optics are quite useful for tricky situations when you can't quite get in the perfect position on an enemy. With good timing you can finish off the hacked enemy without their friends alerting. These are particularly good when an enemy is leaning against something, preventing you from getting behind them, or if they will hear or see you on your route of approach.
However, the coup de grace IMO is Whistle. You will have to use the terrain to your advantage, but whistle will make the hacked enemy suspicious as if they just heard a distraction at your location, and they will come to investigate. It will not alert their friends, however. The range is limited, and they don't always follow a strait line to your position, so be sure to mark them in scan and be ready to move. There is no tall red grass like in Horizon: Zero Dawn nor takedowns from the front so it's less OP than whistling in that game. However it can easily break up groups otherwise impossible to take down stealthily without it, pulling an enemy away from the pack to a place of your choosing. You simply need another nearby location to hide until you're ready to strike. The two best ways of doing that are to find either a piece of cover such as a pillar you can move around completely, (so that regardless of which way the enemy goes around it you can come up behind) or something high you can get on top of. Enemy vision when they are not in combat is very very narrow vertically. Even if all you have is a corner to hide around you if you time a reboot optics right you can blind them before they actually alert and take them down. This also makes it much easier to dispose of the bodies before pulling the next one and since you don't enter combat you can recharge all your RAM units.
Misc:
Having a Synaptic Accelerator slow time when you're detected can be handy as well.
Also highly recommend double jump or charge jump as it gives you vastly more options for traversing the map and getting the high ground, which is extremely good for hiding and marking enemies.
If you can't find or make a better weapon, upgrade what you have to increase the damage.
If you need weapon xp don't snap necks. Choke enemies out and finish them with your weapons for some weapon xp.
If you're a hacker cameras are your friends instead of your enemies, letting you potentially see, mark, and hack every enemy in the area. However, there's a glitch that can be problematic... If you have enemies marked to keep track on them and a friendly camera see's them it will essentially temporarily mark them while in vision, but if the enemy moves out of the camera's vision this will often unmark enemies even though you manually marked them. You may need to disable or destroy the camera if you need to keep a particular enemy marked, though once you've learned their patterns it's usually easy to just keep tabs on them and remark them from time to time as needed.
Take out patrolling enemies first, then the static enemies are much easier to deal with.
Sometimes not hiding the bodies is a good idea. Enemies will become suspicious and investigate a body. This can let you predict exactly where they will go when they see it and use them as bait.
If you're in a public space sometimes you can get closer by not sneaking so you don't look suspicious, but if you get too close they will alert on you loitering in their face anyway.
You can shoot explosive objects with silenced weapons to kill or soften up enemies. They go into alert, but won't know where you are.
Mainly... stack those modifiers. There are sooooo many things that can enhance your damage in various ways.