You should sign out of your Apple ID (in the AppStore, iCloud, and Find My Device) on any device before getting rid of it or replacing the hard drive. Otherwise you risk losing an activation count for apps you've downloaded.
In the instance under discussion, isn't there a difference between device and hard drive for the purpose of Apple's counting? If the replaced hard drive is not used anywhere else, then the count has not changed. Otherwise, more users would be burning up their allocation just from restoring via clones or TM backups.
I don't know Apple's process here, but I would imagine that for counting they would look at some kind of hardware ID, and if that does not change, then the count does not change.
