Apologies for the delay in adding to this. I had a terrible time removing the Carbon Copy Cloner Safety Net folder and have learned that was a result of Apple's recent "System Integrity Protection", or SIP. However, after deleting the folder and restarting I had only a single instance of Cookie in the Menu Bar but the next restart brought back two versions of Cookie.
I had no drives either mounted or even turned on. What I did notice is that Cookie showed as a Login Item:
so what I did was:
I unchecked “Open Cookie at Login”
however, this still left the Cookie.app login listed in ~/Login Items
“hide” was initially checked but I have unchecked it.
Removed the ~/Login Item/Cookie.app
relaunched Cookie and re-selected “Open Cookie at Login”
This does not recreate the Login Item in ~/Login Items
After a restart the Cookie Login item no longer appears in ~/Login Items
I also have had no repeat instance (so far at least) of double Cookie apps in the Menu Bar.
Obviously Cookie is using a different method to launch itself at Login other than including it in ~/Login Items so perhaps my Login entry was from an earlier version of Cookie and never got cleared when Cookie was updated?
For the moment this seems to be resolved. I have restarted a number of times this morning and no double instances of Cookie have appeared in the Menu Bar.
Still, the question remains for me as to why this would seem to randomly begin occurring in the first place.