It is implemented in this commit.
I think it is sufficient enough, though you still cannot make subfolder in normal folder or subfolder in subfolder.
From now, bookmarks in toolbar are no longer present in Bookmarks Sidebar, as it is unnecessary and it also frees some space for your unsorted bookmarks.
This feature will be included in next version (1.0.0 stable)
Note: If you are building from git, you may need to either delete your profile (~/.qupzilla) or change your profile version to 1.0.0-b4 (in ~/.qupzilla/profiles/yourprofile/version file) in order to update your profile database.
You can check how it looks on following screenshots:
|Toolbar with 2 subfolders|