This plugin allows nesting of shulker boxes, I have used it personally for some time and decided to post it now.
You can open shulker boxes by right clicking them in your inventory, and you can shift right click (or just right click depending on the version) an empty slot to go up to the previous layer of shulker box you were in.
Shulkerception.use is the main permission node.
This is update-safe, the system uses nbt data for storage, so if you end up removing the plugin the items will not be lost.
Please note that if you store too much unique data in the box that you will cause a crash, so be sure to adjust the nesting depth in the config as would be appropriate for your user base. Mind you, it took storing an entire mega base worth of items in a single box for it to cause this crash on my end.
This has built in safeguards for epicbackpacks and slimefun.