How to store custom ltspice symbols/schematics in a subfolder?
Hierarchical symbols are made so that they reside in the same place as the top level schematic. What you are doing is you move them elsewhere, LTspice can't see them where they are supposed to be, and you get errors.

OTOH, if you create regular symbols (not hierarchical), then you can move them around and set a custom path in the settings, but you'll still have to pack them together with the rest of the schematic in case you need to move/send/etc your project.

TLDR: Hierarchical symbols need to be in the same folder, regular symbols don't. It's up to the user to make the choice.