analyse disk space usage of an encrypted home directory

You said "..baobab just keeps scanning endlessly without counting any data when I ask it to just scan my home directory..." so you might have already tried this, but for others with this problem; I found that while selecting the root directory just showed me a bunch of ambiguous ENCRYPTFS files, selecting my home directory from the "Devices and Locations" screen solved this problem.

On the first "Devices and locations" screen, click the three line icon in the upper right, and hit "Scan Folder..." in the menu that pops up Select your home folder, and baobab should scan it.

Note that I only tested this while logged in to my account, and that it took a very long time (1hr+ for 220GB) which might account for your "endless scanning".

For me, just running baobab ~ was enough to have it properly check the home folder (mounted .ecryptfs volume).

I personally found that using ncdu worked quite well.

You can install it with the command sudo apt-get install ncdu after you enable the Universe Repository