You are using namespaces like folders, but they are namespaces. See:
Different ways to structure data
The contextual sidebar: query current page and organize pages in indexes
You can manually organize the Markdown files in subfolders, Logseq will just ignore the folder structure but it would be nice if we could somehow access this structure from the app. The problem is that people would ask (and they already do) to use the folder structure to disambiguate files/pages with the same name. Allowing that would mean we are back to the simple hierarchy of the file system instead of just using the outliner. But again, if what you want is just files with unique names organized in different folders, just move them manually.