How to organize a shared cache for qsys systems?

I would suggest Not to treat a parent .qsys as self-contained through IP_FILE. For nested Platform Designer systems, use a directory that preserves the original relative structure, and configure that directory through IP_SEARCH_PATHS or .ipx files.

The parent .qsys stores child-system and component metadata, including path information. IP_FILE registers a specific .ip instance with Quartus, but it is not a universal override for resolving every child referenced inside a .qsys.
 

In short, use IP_FILE for project-level .ip instances, and use the project IP search path or .ipx files to discover _hw.tcl defined components. Preserve the nested .qsys dependency structure separately.

2.6.5.2. Defining the IP Search Path with Index Files
https://docs.altera.com/r/docs/683609/26.1/quartus-prime-pro-edition-user-guide-platform-designer/ip-component-description-files
 

The Quartus® Prime software identifies parameterizable IP components in the IP search path for the following files:

• Component Description File (_hw.tcl)—defines a single IP core.
• IP Index File (.ipx)—each .ipx file indexes a collection of available IP cores. This file specifies the relative path of directories to search for IP cores. In general, .ipx files facilitate faster searches.