How can I identify all the empty folders on my iMac?

Because I am little bit obsessive-compulsive I have two external drives for backup - one for Time Machine and one for Carbon Copy Cloner -

That's all? 😄

I really, really wouldn't concern myself with empty folders. Not only is the space they occupy negligible, they are only backed up once. The same goes for any file that remains unchanged. Only one backup copy exists, no matter how long the TM history may be.

The other reason is that although most Mac apps (and in fact, every Mac app that I experimented with on this Mac before providing my reply) will not let you delete a folder, even an empty one, if it is required by that app. Attempting to delete it will result in "permission denied" or words to that effect. Of course I have no idea whether you have and depend upon some apps that aren't as well thought-out. As a matter of fact many years ago I deleted some empty Library folders for reasons similar to yours, and was rewarded by a runaway macOS process that (apparently) depended on their presence. As a result the Mac began to perform poorly. Manually recreating that completely empty folder fixed the runaway process.

Recent macOS versions protect themselves against such user-inflicted damage, so you can't do what I did any more. It's just an example.

Sure, but I recommend deleting only empty folders that reside in your Home directory and its subdirectories.

Important: Read the caveat at the end of this reply before doing anything. Don't say I didn't warn you.

Use the Terminal app: Terminal User Guide for Mac - Apple Support

find /Users/john -type d -empty

... where "john" is your "short user name".

The above example will show you all the empty folders in your Home directory including all its subdirectories.

Once you see how many there are, you might want to think twice about deleting all of them. The reason is that some apps might not cope well with directories that it expects to be present, even though they may be empty. Certain apps are certain to be sloppier than others in that regard, but really well-written and robust apps are rare.

After giving that caveat some well-deserved consideration, you can modify the above command to delete them:

find /Users/john -type d -empty -delete

... and just like that, they'll be gone.

There is no "undo", so if you mess up the above command or it deletes an empty folder that an app nevertheless requires to be present, your only recourse is to restore a Time Machine backup. To learn how to use Time Machine please read Back up your files with Time Machine on Mac.

I saw your question and remembered I'd seen it answered in another discussion. Here it is:

Empty folders 

Sure, but I recommend deleting only empty folders that reside in your Home directory and its subdirectories. 

Important: Read the caveat at the end of this reply before doing anything. Don't say I didn't warn you.

Use the Terminal app: Terminal User Guide for Mac - Apple Support

find /Users/john -type d -empty

... where "john" is your "short user name".

The above example will show you all the empty folders in your Home directory including all its subdirectories. 

Once you see how many there are, you might want to think twice about deleting all of them. The reason is that some apps might not cope well with directories that it expects to be present, even though they may be empty. Certain apps are certain to be sloppier than others in that regard, but really well-written and robust apps are rare.

After giving that caveat some well-deserved consideration, you can modify the above command to delete them:

find /Users/john -type d -empty -delete

... and just like that, they'll be gone. 

There is no "undo", so if you mess up the above command or it deletes an empty folder that an app nevertheless requires to be present, your only recourse is to restore a Time Machine backup. To learn how to use Time Machine please read Back up your files with Time Machine on Mac.

Credit goes to John Galt’s Profile - Apple Community

When you start deleting files/folders that you do not understand what they are used for, you are likely to create problems for yourself. Don't do it unless you know precisely what you are doing. Empty folders take up virtually no space, so they do not cause any problems.