Disk ejected but still show up in Disk Utility?

Solution 1:

Weird as it is, this seems to be the solution:

  1. Remove the disk from Time Machine's list of backup destination drives.
  2. Remove file tmbootpicker.efi from the drive's root directory.
  3. Remove file /var/db/volinfo.database
  4. 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.