I think that neither yourself nor your players, are playing Numenera. Warning signs such as "dungeon-making skills" and characters able to use 5 level of effort (wow!) makes me think that you are trying to play D&D with a different world and system. This will not work, as you clearly found out. This is an paradigm problem.
In any case, the true path to Power in the Cypher system is, well, the cyphers.
The whole point of Numenera is to use cyphers like they went out of fashion. After all, you gain many new ones all the time. Traditional hoarding will hold you back and make you less powerful. This needs to be clearly explained to the players: "Do not hoard, spend!"
So, do a silly one off encounter with different cyphers: each player plays their character but with a random set of cyphers. The aim is to defeat the obstacles in their path using those cyphers. The next iteration has new cyphers so forces the players to adapt. This should not take more than an hour per round. Do a few, and your players (and yourself) will get how it work. The aim here is not to defeat all the obstacles, it is to get used to spending cyphers. It should forces the players to think outside the box and come up with new and fun uses for their cyphers.
A good such encounter might be a physical fortress, a hostile guardian, some social interactions, and a combat against people using the same cyphers themselves in each iteration.
During game play, offer them many new and interesting cyphers. So, unless they use theirs, they cannot pick up the new ones. Sure, they can discard some to pick a new one but really, where is the fun in that? You are not playing a tactical board game (neither sarcasm nor insult implied) but a story game. Make sure you players know that their characters are not going to die because they spend that cypher last session.
If the players have a healing cypher (say it regenerates limbs), then clearly your next GM intervention cuts a character's hand. Said player can either take it, gleefully get a XP, and regrow a limb or be boring. Now, of course, another GM intervention that turn said arm into an obsidian black animated sculpture might work well -- think Hell Boy.
As a GM, you know what cyphers they have. Suggest to them to use them: "Alice, your character has a cypher that allows her to float. That might be a good way to get your bearings in this weird wood."
Finally, you need to talk to your players and convey the idea that they are responsible for building the world around them as much as yourself. Cyphers are one way to make it the commonly shared story more interesting.
You said:
I think the core of the problem is that we are playing out every awake moment of the characters - there are no visible scenes, only continuous flow of character actions and world reactions.
I had a campaign very much like that a while back. It took them multiple sessions to just do one task walking around an island. They didn't mind at first because just the experience of camping in-character was entertaining, but we did eventually agree to settle into a breezier pace.
In my experience, the key is to think about movie pacing. Do they show every waking moment? No, they say "Let's go to a place" and then the next scene is "Ok, here we are at the place, let's do this!" You can absolutely do the same thing: "OK, about 4 hours [or even 4 days] later, you arrive. As you approach, you hear..." Basically, get to the good stuff.
Note that this approach requires trust from both parties. You have to trust that on the one hand, your players will interrupt you if they wanted to do something particular; and on the other, that their characters are reasonably competent and act like it. Your players have to trust that you won't pull the old "You didn't say you got dressed this morning so now you're all naked and freezing" - if the adventure doesn't specifically call for resource management as part of the tension, and players want to clarify things a little bit retroactively, let them.
PC: "OK, I offer the princess a drink."
GM: "A drink of what exactly?"
PC: "Of water from my waterskin, which, it goes without saying, I filled
up at the well before we left town."
GM: *the briefest of pauses to consider if their character is like that* "...Right, naturally. She accepts gratefully."
If you and your players don't want to spend time listening to each other fill waterskins, you have to actually let that go without saying. That doesn't mean you can't show more mundane parts of life, but usually you'll do a bit of that towards the beginning as people get to know each other and establish routines, then count it as done and gloss over it the next time. For example, you can ask them how they do watches once if that's applicable, let them argue it out (preferably, for my taste, in-character), and then assume that they do them the same way in the future.
In my case, part of the problem was trying too hard to avoid metagaming - so I'd roll lots of random encounters including harmless animals, but the players would treat each one seriously and look around for danger, which took up quite a bit of time. It's okay to assume that's going on as you're traveling, and only actually ask your players to roll to see if they notice any danger when there's actual danger to notice. Along the same lines, you can ask in very broad terms if they're going through a dungeon carefully searching for traps/treasure vs. moving quickly (the DMG has specific guidelines for this), and then just roll for them, use passive Perception, or ask them to roll quickly when there's actually something to find. This saves your players from describing, in detail, how they search each room... which can be part of a good game that tests player skill (you don't find the gem in the dresser unless you actually tell me you're searching the dresser) if you're all into it, but definitely slows down the action.
In general, just remember that you don't have to roleplay everything out just because it happens. For skill rolls, the Angry GM (warning: he is indeed angry and a bit vulgar) advises to only roll if there's a chance of success, a chance of failure, and a consequence for failure. You could almost say the same thing about roleplaying - only make the characters go through a scene if there's some decision to be made, some opportunity for the characters to really show who they are, and/or some way they could really screw things up and then save the day. That's what good stories are made of, right?
Best Answer
Preface: I haven't played Savage Worlds so I'm unfamiliar with the details.
I've been playing in a FATE Core game recently and Troubles sound pretty similar in description. For FATE, they had the mechanic of compels where anyone could suggest a way to bring up your trouble in an interesting way (e.g. maybe you have "a lover at every port") and someone might use that to say one of your past lovers shows up and complicates a situation. If you accepted it, you would get a FATE point (which sounds like a Benny) and if you declined it, you would have to pay a FATE point to avoid it.
A similar option could be done here; you (or anyone could suggest!) could bring up a situation where their Hindrance is important (e.g. "this guy annoyed you before, I'll give you a Benny if you start a fight/try to sabotage him") and offer them a Benny if they act in accordance with it, or they pay one if they do not. At least in FATE, this ties all of them into mechanics a little bit and in your situation would make the fluff ones have a little more mechanical teeth. It does require you (if no one else is) to come up with said problems, but likely you are already doing that.
Additionally, I treated Troubles (and thus Hindrances) as something the player picks to say "this is something a want to do" AND "this is something I want to cause interesting problems." This means that the players should avoid picking Hindrances they don't like; if I hate fighting, I shouldn't pick a Hindrance around fighting. If a player did but it turns out they aren't liking it and trying to avoid it at all times then I would have a conversation with the player about their character and what they want to do in the game. When I came up with my Trouble, it was a result of a conversation between me/the DM so we could figure out what would work best for both of us. This really helped ensure we both knew what we wanted out of it and probably would help here as well.