So first thing's first, I'm new to clicker training but it has massively helped my aggressive pony and my fearful draft mare.
The first thing I'll mention is about horse's not connecting the dots between the action and the reward - well that's EXACTLY what the click is for. I use a smooch noise so I don't need to carry a clicker, but either works. It's a bridge for the horse to know "this right there is what I want" - it buys you time to get the treat out.
Of course they need to learn what the click means, I do this at the same time as teaching a horse not to mug for food.
I'll start in the horse's stall (I've never had to, but in cases of aggressive horses you can start outside the door) with my pockets full of tiny treats, bits of carrots or hay stretcher pellets. Of course the horse will naturally try to mug you, I'll ignore soft mugging, stronger mugging will be met with a growl or a swat, depending on the severity. Normally within the first minute the horse looks away for some reason or another, a noise or they get bored or anything. The moment they turn away I click/smooch and treat. I always treat arms length away and mostly I do it just behind their chin so they need to back up a step to get it - this reinforces the boundaries. This teaches them that click=treat and that they need to be respectful to get the treat always
The next skill I teach is touching a target, I use a crop with a duct tape rose on the end for visibility. I hold it out and most horses will sniff it out of curiosity, my mare was horrified of it to begin with though. With the curious ones I just click and treat when they touch it, still arms length and still behind their chin. With the fearful one's I'll reward steps closer to it, with my mare I touched it to her nose then clicked and treated till she got the concept, then she started touching it on her own. They quickly learn to touch it high and low and on their sides to help with stretching, they'll follow it at the walk and trot, and it can be used to help teach many tricks like backing up, bowing and anything else.
I typically do 3 sessions, 5-10 minutes each a day. The gap gives the horses time to calm down out of the food excitement and time to process what they learned, always the second and 3rd session I'll see remarkable improvements. Most skills take only a couple sessions to really nail in.
It may seem like your clicking/treating for tiny things, but each skill builds on the last, eventually you only need to click/treat for the final product.
I started by teaching my pony to touch the target, then he had to follow the crop, then he had to follow the crop at a trot, then he had to follow it and go over a jump, now he gets a big click and treat after an entire course.
You can teach them to fetch in just a day, first touching the object, then chasing the object, then mouthing the object, then biting/holding the object, then holding/carrying the object, then bringing it to you. My pony will get his halter off the side of his stall and hand it to me now. XD
It can also be used to desensitize items, like tarps - clicking and treating interest in the tarp, then touching the tarp, then standing on it, then being near it picked up, touching it picked up, being rubbed by it, letting it be on them.
Each skill gets amped up, so you aren't giving treats for millions of little things, but it takes time and work to achieve these.
I could go more into detail and am happy to answer any questions, but here are some videos I used to help learn.
There are 3, getting started, ground work and under saddle. Video 1
There are SO many great videos online that explain it better than I could. But I've taught our blind mini to come to the sound of her name, to take high steps when she needs to go over the door sill or ground poles or anything else, to back up and side pass and essentially dance with all verbal or phsyical/touch cues.
Yes treats are an artificial aid, they aren't natural, but neither is pretty much anything else we do with horses. But the behavior, when done right, doesn't require the aid. Like I said each skill is built from the last. I don't need to click/treat for my horse turning her head away ever anymore, but she doesn't get her treat if I clicked and she decides to mug me. I ask my mare to back up regularly throughout the day, when I go into her stall a million times in and out or when I need to go around her front or for any number of reasons, I don't click treat for that - she knows that skill. But when I'm training if she does an exceptional back up, more than a few steps or a very high quality back up with just a verbal command and no physical cue, I'll reinforce it. My mare will come to me and follow me anywhere, treats or not, but if she does something exceptional or new, like trotting to keep up with me, she'll get the reward. So once a skill is learned they only get the reward for exceptional use of it, or if it's starting to get shakey, but typically they only get the reward for the next step in the skill.
About whether or not it makes a horse friendlier. Clicker training will not change a horse's personality, nothing will - but it will change the way they act AND the way they see people.
The way I picture it is like we're the boss, if your boss only got after you when something needed to be done or if you did something wrong, but never said or did anything if all was well - then every time your boss comes over you know
you're getting more work or more complaints about not doing something well enough. But if your boss asks you to do something and you do it well, and he says "good job" or shows you appreciation, maybe earning you that raise you've been working for - it'll be worth it, you'll be more eager to see your boss, even if he does have work for you. You may even WANT you boss to come give you more work because it means more responsibilities, more ways to prove yourself, and more rewards (money).
I think horses are the same way, of course BALANCE is the key, mixing negative and positive reinforcement (removal of pressure + addition of a reward) I find is a great way to train most horses.
But every horse is different
every horse will need a different balance. Finding that balance is up to their handler.
I've never found clicker training to cause any negative results, other than perhaps my horses are a little too excited to come see me, even if I'm just walking by, not going to see them. But I've taken things slow and made sure not to let my horses ever think they could be rude.