Regardless of true/false empty boxes always stack as of 1.21. This causes hopperlines for distributing boxes to break since all the boxes trickle down to last hopper or container.

In 1.21 (Carpet 1.4.147+v240613), with emptyShulkerBoxesStackAlways true and stackableShulkerBoxes true, I'm getting behaviour stranger: full Shulker Boxes are stacking, and due to MC-270846 (Mojang wontfix for some reason???), it's reporting 1 full Shulker in the slot in the Chest, but picking the item up with the cursor or moving it into your inventory reports the stack size.

I haven't changed these settings since 1.20.4, where I had empty Shulkers stacking and full ones remaining unstacked. I'm commenting here because I believe there might be a larger underlying issue in the emptyShulkerBoxesStackAlways code perhaps, and this is another symptom—but I'm just guessing.

Edit: +1 to also being able to recreate the actual issue here btw; I have emptyShulkerBoxesStackAlways set to false now, and it's fixed the issue of full Shulkers stacking, and empty Shulkers stack still even though they shouldn't. It works for me because this setup mimics how it worked with emptyShulkerBoxesStackAlways set to true in 1.20.4—but I'm taking advantage of illegal behaviour here from the mod.

+1 for visibility, same issue for me with empty boxes always stacking in hoppers and containers