I've tested a data pack with a loot table, and in doing so removed a Shulker Box which generated inside of a chest as I wished.

I placed the shulkerbox to examine its contents as set with BlockEntityData{}, and when I entered the Inventory of the Shulker Box, an empty one re-appeared in my hotbar.

The same issue occurs with the vanilla chest from which the Shulker Box generated, but not my personal inventory, so I assume the bug is limited to the Inventory for chests.

The box in question is red_shulker_box, if it turns out to be that specific.

Players being able to dupe shulker boxes that easily is going to make my life crazy, hahaha   Thanks for everything.