This is a bug in the disk analyzer utility. It is misrepresenting the amount of storage that's actually being used on your disk.
The files that are actually written to disk (if you're using Ubuntu's Encrypted Home Directory) are located in /home/.ecryptfs. The files and directories you see in your $HOME are actually a virtual representation of your encrypted data. It's a phantom view of your decrypted data that the Linux kernel presents to the rest of the operating system. Rest assured that it's not taking up twice the disk space.
Full disclosure: I am the author of Ubuntu's Encrypted Home Directory feature and one of the current maintainers of eCryptfs.
I had this problem on 14.04 using the gnome-session-fallback desktop. After trying the other solutions (removing MimeType=inode/directory; and editing /usr/share/applications/mimeinfo.cache) what actually fixed the problem was to run this command as your user:
xdg-mime default nautilus.desktop inode/directory
By default it is set to use nautilus-folder-handler.desktop, which for some reason ends up launching the dreaded baobab.
Best Answer
This inconvenience only happens if you click on the first option (
/
). To avoid this:Home folder
)This will show disk usage for your home folder only, but with the human-readable names.
Enhancement request on Launchpad