Hi @vmanera -
Are you finding that the web resources in sub-folders are not accessible via a web browser? The Admin UI doesn't expose sub-folders in the File Manager, but if you're placing resources in sub-folders from the command line, they should still be available via the web browser (v12.x+) at URL locations like:
https://SEARCH-SERVER/s/resources/COLLECTION/PROFILE/subfolder/style.css