I had the exact same problem on one of my virtual boxes. The problem baffled me for two years and I just added more space to the box a few times to fight it as I couldn't solve the issue. It wasn't the inodes, deleted but open files or anything common like that.
The problem was my mounts. I had occasionally failing mounts combined with crontabs that accessed and wrote data to those mounts. Do you know what happens when you accidentally wrote let's say 200gb data to /mnt/a and then later mount a drive over that mount point? It magically 'disappears' as you'd exclude that mount from the calculations.
Might be you don't have anything mounted and none of the above is useful to you. But this solved my issue and it's quite curious and silly. Just set up mount points to not be writeable and problem went away.
I did the same search some six years ago for our company and ended up with MediaWiki. We had two requirements: ACL and Ease of Use for non-technical people.
Both of the above are missing in the plain MediaWiki but extensions helped out. There were few different ACL extensions and I can't remember which one I picked. Ultimately now we have the secret access controlled side of the wiki and the internal "public" side where everyone can access.
VisualEditor was a key extension. It's a rich text editor with minimal fuzz for MediaWiki. Users never have to deal with the MediaWiki markup which is a must for non-technical users.