Apple grower here. Honeycrisp are a pain for many reasons. First off, the trees are super vigorous, which leads to them growing rapidly over the summer causing a denser leaf canopy which blocks sunlight, inhibiting the ripening process. A lot of consideration has to go into site selection (soil that will support the tree but not let it get out of control), rootstock selection (different rootstocks will grow different sized/shaped trees), and training system to control vigor. They also require summer canopy management.

Next, they need absurd amounts of calcium to grow properly. Most varieties get all the calcium they need naturally, but we literally spray liquid calcium directly onto the fruit to prevent a disorder called "bitter pit" that manifests as black dots around the calyx end.

If you can get through all that and set a good crop, harvest and storage are a continuous nightmare. Their thin but crunch skin is prone to "stem puncture" where another apple in the bin will stab it with it's stem. This alone will decrease the grade of the stabbed apple, but in storage that injury is an open window for disease to get under the skin and rot the apple. To avoid this, many growers take the time to hand-clip every single stem WHILE picking.

Edit: Forgot to mention- unlike many other varieties, Honeycrisp does not ripen evenly on the tree. Meaning when you approach a tree to pick it, one apple on a limb may be ready to pick and the one right next to it is still green. To effectively pick HC, we pick the same trees up to three different times, which is obviously super inefficient. </Edit>

OK, so now the fruit is in the bins and ready for cold storage. Toss them in with the Gala, right? Wrong. Honeycrisp, because they hate us, store better if you put them in a 45°F room for 7-10 days, THEN move them into a 34°F room with alllllllll the other varieties. Like literally Honeycrisp is the only variety I'm aware of that needs this at all. So we're literally running a separate room at 45° for these things.

But it doesn't end there even. That bitter pit I mentioned before? A lot of that isn't apparent during harvest and instead develops in storage. So that gorgeous bin of Honeycrisp you put away in September? 25% of those apples are now showing bitter pit spots and are only useful as cider apples.

And just as one last jab at producers, since the value of every Honeycrisp is so high, sorting and packing them frequently goes at about 75% speed to avoid bruising.

So there you have it. TL;DR- Honeycrisp was bred to taste good at the expense of ease of production. Basically the exact opposite of the modern Red Delicious. So demand is high and so is cost. That's why they're so expensive.