This article is about the history of the shulker_boxes.png-atlas file. For a comprehensive history of block texture changes, see Java Edition history of textures.
shulker_boxes.png-atlas is a procedurally-generated texture atlas used to store textures for all shulker boxes.
Shulkers themselves do not reference this atlas, nor do their bullets. Notably, this means that while shulker boxes can be animated like many other textures, doing so will cause shulkers to appear completely broken in-game.[1]
As an optimization to resource pack loading, everything in the relevant directory is compiled into this atlas, rather than only those sprites which are used by the game.
Minecraft also generates mipmapped versions of this atlas, for unknown reasons. They are not used by the game at all - only blocks placed in the world which use the json model system use mipmapped textures.[3]