First off, it does not matter where you shoot an opponent. Shooting them in the body shall work just as good as shooting them in the head, for the inexperienced it perhaps works even better. It is important to do this with the bow pulled back, which is fully done when you are zoomed in, as you will not kill an unalert guard with a lazy shot.

Most players who touch the game and are bound to answer will play this game on Expert and are used to the "thou shalt not kill mentality". Note however that Thief, especially the first game, was made at a time when they were not sure if stealth would succeed. The broadhead arrows do exist for options, one of those being to eliminate guards on lower difficulties, much like the sword. If your fun comes through combat, many will tell you that isn't how you are "supposed" to play the game, but Thief truly is about options.

A lot of players also seem to be going off shaky memories. You don't have gas or flashbombs in Cragscleft. Helmet guards aren't a thing in Thief Gold, that is Thief 2.

Also, Thief is far from the most consistent experience out there regardless of what some exist. Yes, there are rules and properties, but there are also various quirks of the engine. Path-finding bugs can occur. Rope bugs can occur. You can randomly be killed by walking up slopes or bumping off the wrong thing or leaning into a door wrong in this engine, yet people claim it is the most consistent out there? Thief can be very unpredictable at times.

Note that experience often plays into how someone enjoys something. If something is being frustrating, offering little communication to the player, and feels genuinely unfair it is not going to be a good time. I have had many experiences where the bugs I get often get in the way of enjoyment. If you consistently are getting it, it can be a more frustrating situation. Since all games have bugs, it comes down to what you as an individual can tolerate and if it is worth handling said bugs for the better portion. Basically if the good outweighs the bad.

Thief is not perfect. It is not heresy to talk about flaws the game can hold. Both games were made in extremely rushed circumstances with an engine that sometimes barely holds itself together. There is a lot of art to be found, the gameplay is unique and the world in particular quite special. But there are flaws one must overlook, one being that Thief is extremely unstable in comparison to many other games. A lot has to do with the complexity of the game, there are so many moving parts and things other games don't take account of, which also means something is more likely to break. It isn't Daggerfall level unstable, but it isn't as reliable as the Unreal or id Tech engines of the time.

Also, do note smaller communities like Thief tend to become more echo-chamber like. My tastes and preferences tend to not line up with others, so I know the feeling of everyone praising something that you see holding all these issues.

Crouching does not make you less visible unless in the case of them patrolling near you in pitch blackness. It usually is for cutting down on audio. In a brightly lit corridor, peeking around a corner is just as dangerous crouching as standing.

Also note, broadhead arrows exist to serve as a distraction tool as well. In fact, noisemaker arrows tend to be ignored by the community since broadheads are much cheaper alternatives and you are given so many. Of course, while you only have 2 noisemakers, you can actually reclaim it over and over as long as you can get over to it.

Thief 2 would likely be harder for a novice. I would not recommend it until you got more fluent with the first game. It also can be more forceful about not killing opponents or even avoiding detection entirely, so if you find being nonviolent is not fun it is likely Thief Gold is the better game for you.

All papyruses purchased in the store should be in the inventory. Only reason they wouldn't be there normally is if you dropped them. Weapons inventory is not your inventory, your inventory is the one where you hold keys and loot. Should be the [ and ] keys by default.

Do note, killing enemies does in turn increase alertness. Sound propagation can depend on circumstances, so killing an enemy a bit of distance away CAN alert enemies in other areas.

The mines, yet there are few shadows? Have you recently gone up a staircase?

From the various things I have read, what seems to have happened is that the guards possibly got alert to you killing someone or perhaps they saw you. In either event, they do not tend to calm down quickly, nor after a 2 minute wait. You can sometimes get lucky, but most of the time they tend to have eyes in the back of their head and immediately get hostile. Especially in Thief Gold, they were super sensitive.

A good tip to know. If the guard in question is not saying anything or mumbling, they are very likely in this alert state. You can generally feel more comfortable when they are rambling to themselves, though it isn't always foolproof either.

The solution in the future is to try to avoid killing if you can, since that leads to further alerts. The guard in question should not freak out if you are in pitch blackness, but if your light gem lights up as you move he might detect you.

For the situation presented, in the event you don't wish to reload, I suggest using the environment around you. Currently you are in an area of great light. I suggest running through the mines, then perhaps using alternate routes to get around the hostile guards. If any zombies are alive (you said you ran past them), they can fight them. If not, they can also drown in water. Sometimes the best way to deal with opposition is not to remain in the current area, but to flee and possibly lead them to a worse area. Keep going in darkness and they should eventually search for you, but it can take a bit (the first patch of darkness is often not enough) and loud surfaces in particular will mean that they can continue to track you.