The cache.cpk included with Persona 5 is a copy of most elements from the data.cpk, for the purpose of being installed on the console's harddrive for faster loading times. However, this was never removed from the digital PKG, in similar fashion to Persona 3 Portable's MEMST.cpk. It can be safely deleted from the USDIR folder containing it without any consequence.
Modding
Although useless for the digital consumer, it has some (limited) applications for modding. By matching the filestructure of P5's data.cpk, you can create a custom cache.cpk that will override the contents of other CPKs, which is a much simpler and less direct way of editing the filesystem. However, the inclusion of directories and files from the Persona 5/ps3.cpk will result in the failure to load any content from cache.cpk.
Because of this, the recommended method of modding is to use the patch3ps3.cpk instead (for Japan using the latest update) or by using the Mod Compendium to generate a mod.cpk containing only your modified files.