The items in the /Volumes directory are the equivalent of what you would see in the /mnt directory on Linux. They are temporary stand-ins (sometimes called "device special folders") for the volumes you've mounted. However changing these temporary names won't affect the actual volume names because they are merely stand-ins for the real volumes.
The name of a volume isn't stored in quite the same manner as the name of a folder, so when you see the volume name in the /Volumes directory you're seeing a "special folder" whose name has been borrowed from the volume name which comes from the "volume header" of a given partition.
Try renaming two or more volumes in the Finder so they all have exactly the same name and then list the contents of /Volumes. Pretty interesting, eh?
The only way I've been able to discover to change the name of a volume is through the Finder, and of course the Finder wisely prevents you from using a name beginning with a period. If you're trying to make your volume invisible you'll need to find some other clever trick!