Encrypting your homedirectory is generally not a bad idea.
With Ubuntu’s implementation it’s working out of the box.
However, if you are running processes from a “screen” and these processes require data from your homedirectory, they will fail whenever you log out from your ssh session.
It’s because your homedirectory will auto-unmount whenever you log out (eventhough the screen will continue to run).
To NOT auto-unmount your homedirectory, you can remove or rename the following file:
.ecryptfs/auto-umount