Disk ejected but still show up in Disk Utility?
Weird as it is, this seems to be the solution:


Remove the disk from Time Machine's list of backup destination drives.
Remove file tmbootpicker.efi from the drive's root directory.
Remove file /var/db/volinfo.database
After restarting and able to mount the drive again, re-add the drive to Time Machine.


Ejecting the drive seems to work now — it finally disappears from Disk Utility's list after the USB cable is unplugged.