The “favourites_count” field indicates the number of “favorite tweet” objects the user has created (not necessarily the number of times a user has favorited something).
If a user creates a favorite, it will be counted in that number. If a user destroys a favorite, it will be (eventually) decremented from that number.
If the user has favorited a tweet belonging to a user that has deactivated their account, eventually the tweets belonging to that user will become deleted. Once the tweets are deleted, eventually the favorite objects associated with those deleted tweets will be deleted. Eventually, the number of favorites in “favourites_count” will decrement to note the removed favorite objects.