Why would you want to do this might I ask? Seems rather pointless. Also seems a touch dodgy as (buggy?) applications could well rely on those folders existing.
Sometimes I have a USB stick that is getting full or a portable HDD. I take the entire contents and move it to a directory on a larger external hard drive. I then pick through the directory deleting what I don't need to keep and reorganizing what I want to keep. It is easier to sort through the directory if I can first cleanup all the empty directories.
It's just a convenience thing in this case.
I often also use it on a directory before archiving it using some non-standard compression program - as those usually allow you to ignore empty directories.