So for us "Close task" doesn't work anymore, looks like you just have deleted the code which processed the button. Is there any replacement for this I don't know or you have just deleted a nice convenient feature which worked fine for some people like we are?

It's probably the correct solution to create ancestor slugs automatically if you so choose. I believe this is what you're running in to?

Our corporate wiki is around 400 documents at the moment, around 15-20% of the documents are rather folders and me or our team members are adding a few new documents per week.
I understand second paragraph is not very easy to do, but first I guess is easy. Is there any reason to make the body for documents obligatory? Why the body can't be just an empty string if the person, who created the document wants so?