Fantastic, thank you for taking the time to write this!

Out of curiosity, how do your typical session prep and the typical session look like, in terms of encounters and story? How much of it is tied to what’s in a hexagon and how much is “freeform”?

Thank you for reading!

On the first question mark: it’s enough to have a general idea of what areas are more dangerous and convey that to players, like you do. You should know what is making an area particularly dangerous and make sure to not scale those specific sources of danger down to the level of the players. Other than that, this is not a videogame, it’s not like every monster and NPC in the area should scale with the danger level of the area or the level of the players. We always need less content than we think anyways: roughly speaking, in d&d 5e we only need 1 fun encounter per hour of session. Not everything needs to be a challenge.

About areas that become useless: in my experience that’s not a problem. When there is nothing engaging for players in a location, the adventure will call them somewhere else. Sure, don’t force them to go through 50 super easy random encounters on the way. Read the room, like a DJ :D

Which brings us to your last point: skipping travel at high level. In general, I would adopt the opposite perspective: not “skipping boring content as needed”, but rather designing sessions so that players go from one interesting thing to another, with transitions and downtime in between. I realize this does not fit the model of the hexcrawl, but the truth is I don’t know how to fix hexcrawls: by construction they have so much filler content. I can’t make that fun. After the first one or two sessions the plot is in motion and you can directly prepare what serves the story rather than preparing the content of the surrounding hexes.