The contents of /run are on a tmpfs — a filesystem in virtual memory — and among other things, it serves as the parent directory to the mountpoint for the volume containing the snapshots, i.e. /run/timesdhift.
Flatpaks certainly consume a lot of space, and in my personal opinion, they’re not worth backing up, because they are completely containerized standalone applications.
You may also want to exclude /var/cache. Anything below that directory is by definition expendable and can easily be recreated.
/home is a directory in the root directory. It is not the same thing as your home directory, which is a directory under /home.
They are hard-links, not files. A hard-link is just another filespec — i.e. filename and path — for an already existing file. See the tutorial below… 
As @Teo said, you should not rely on du for this purpose.