I have one drive that does not show up on the desktop or in the Locations sidebar of a Finder window, but if I Go to Folder, I can see it in /Volumes. Other hard drives, internal and external, show up as expected, but not this one particular USB external drive. I haven't done any more digging into it, I know it is there and my Carbon Copy Cloner does a nightly backup to that external USB drive. It is plugged into the same USB hub as another external dock/drive. When it is plugged into a USB3 port on the computer it unmounts frequently, but that is another issue.
So, for those who can't see the drive in Finder, does it still show up as a mounted /Volume if you Go to that Folder? You can Make an Alias of the /Volumes folder on your Desktop to get to those mounted drives quickly, as a work around.
For example: my OWC Backup is mounted in /Volumes, but I can't see it in any of the usual places the other hard drives show up.