Right now my iCloud account claims that my storage is fully used up by messages, except this is after deleting all my messages and confirming they are deleted by resyncing a new phone and making sure the conversations are indeed deleted (as they aren't coming back on the new phone).
For a long time (might still be the case), deleting entries or search history in Maps wouldn't actually delete them on anything but the current machine - logging into a brand new machine would bring back entries that were supposedly deleted years ago.