(1.18) Using emptyShulkerBoxStackAlways shulkers that have at some point been placed in the world will have 1 NBT tag (NBT: 1 tag(s)). This causes them to not stack with empty shulkers that have only ever been in inventories or in item form.

This tag is BlockEntityTag {id: "minecraft:shulker_box"} and could be ignored by the stacking logic.