Files and folders not visible

These screenshots say very little. Do these 'missing' folders contain images that you have imported into the Lightroom catalog? Lightroom is not a browser. It only shows those folders that contain images that you have imported.

You are, I hope, aware that the Folders panel does not tell you what folders are present on disk.

It reports, for the images that are imported (and only for those), what folders those have been recorded as living in.

So, your first step is to verify that the photos living in these folders have been imported to your current Catalog, and not since removed. This can be done using All Photographs view, in the Catalog panel. That shows a total number (and displays thumbnails) regardless of what folder and drive volume each image's source file is recorded as being stored in. If photos show up in the All Photographs view you can right click and choose "Go to Folder in Library". Perhaps the location they are shown in, within the Folders panel, is different than what you expected to see.

Or if they do not show up in All Photographs, this particular Catalog does not have those photos imported.

That alone would be sufficient to explain why these folders are not showing up. Perhaps, for example, you need to open a different Catalog. Perhaps Lr Classic didn't start out by up-converting your Lightroom 5 Catalog, but rather began with a fresh Catalog; or perhaps, an earlier Catalog was up-converted but this was not the right one that had all these photos imported.

Some of the Folders missing in the "Classic Navigator.jpg" screen shot may be made visible by performing a context-Click on the folder entry and selecting "Show Parent" from the menu.

Does this help somewhat?

Its difficult to see inside someones OS file system and make quick sense of it sometimes . . .