Firstly, where are you looking at the space reported? If it is the Device information page, that doesn't take into account root partition used for the operating system and the recovery partition. That is over 500MiB. The "About" page shows how much storage is available. It is on the second page for my Aura ONE, might be elsewhere the different sized devices. My Aura ONE shows 6.73GB as available.
As well as that, there is the question of whether the sizes that Kobo shows are metric or binary based. My bet is that it is metric. Whereas the calculations you are doing will be binary based. Or I should say, the PC will show them using binary. That would mean the space available on my Aura ONE would be 6.27GiB.
For calibre, where are you doing your count? Are you doing that from the library list and looking at what has matched to books in the library. If you have books on the device that are not in the library, you won't see them. The device list should show all the books.
There are other places for differences that make it hard to match the space and books on the device:
- .kobo/kepub includes any previews, but, they don't show in calibre unless you changed some driver options.
- The .kobo-images directory takes a lot of space for the covers. As well as your books, there will be cover images for any recommendations. These should only have the smaller sizes, but they do take space.
- There are other files involved. The database for that number of books will be well over 100MiB in size. You can use a tool such as WinDirStat on Windows to get a very good display of where the space has gone.
- You might have a few books that aren't in the database. That could be kepubs from Kobo that weren't cleaned up properly, or sideloaded books that weren't imported for some reason. Hopefully the account repair fixes the first. The latter will probably mean that you will see the importing screen when you disconnect the device from a PC even when you haven't added new books.
- Directories can be excluded by the device for searching for books. If you have somehow put an epub in the kepub directory, it won't be imported.
There was another fairly recent thread asking the same basic question. That had some other ideas for checking the space. It is probably worth looking at.