When using a network attached storage device (NAS) like the My Cloud, the top level folders are typically called Shares. The icons in your screen capture that you see for them is how Shares on an NAS typically look.
As to files that are taking up space but are not showing up in visible Shares. First step is to ensure the account you are using as full access to all Shares in the My Cloud Dashboard. That will allow the user to access each share to see what folders/files they contain and to see how much content is in each Share. One can also use the My Cloud Dashboard to review how much content each Share contains. See the Dashboard > Shares tab.
I don’t use Smartware but check the settings of Smartware to see if there is an option to keep multiple backup histories to allow users to recover files from different backups.
If using WD Sync, be warned that WD Sync may be creating a hidden folder filled with deleted files that were previously synced. It allows a user to recover deleted synced files. Use the forum search feature (magnifying glass icon upper right) and search for WD Sync hidden files to find several past discussions on where to find that hidden folder on the My Cloud using SSH (or WinSCP via SSH).