The issue
After importing OneNote Notebooks, all subpages has had their hierarchy broken, because Joplin does not seem to support subpages (See Example 1+2)
The suggestion
Since Joplin does not support subpages, it would make sense to retain the hierarchy by converting the pages of subpages into a subnotebook, where the subpages becomes the pages for the newly created subnotebook.
Pages where no subpages are connected should be left as is, which means that they should be ignored and not be made into a subnotebook.
To see what this could look like, check Examples > Joplin conversion of subpages into subnotebooks.
Examples
1+2: Import from OneNote to Joplin, where the previous subpages have become "regular" pages.
3: Joplin conversion of pages with subpages into subnotebooks and subpages into pages.
Note how the subpages from OneNote has been divided into 4 pages of two new subnotebooks and how the remaining pages, that did not have subpages, has been left alone in the original notebook.
