That sounds odd, n4zty. It might be that there were some hidden files somewere in those folders.
Because folder structure does not (noticeably) affect disk usage. A folder only requires a few hundred bytes to work (it's just a pointer/reference to an inode on a disk, and a varchar array to hold its name), so placing the same file at /root/filename takes virtually the same amount of space as having that file in /root/subfolder1/subfolder2/[...]/subfolder1023/filename...
It's just harder to get to / traverse to that file by following its path
I'd say if you still have an image of that filesystem with all those 0s strewn about, have a look-see using some type of disk analyzer and maybe some cookies/booty/bagsOfCereal might be hiding around somewhere in there!