I think you are talking about something else entirely, you are referring to files this thread is relating to records, but using your examples lets exapnd your theroy.
When you delete a file it is deleted but the space is not used until you either defrag or do a format during that time it is possible to retrieve some of this information depending on the file..
However when you delete a call log or sms then you expect this to be gone from your phone in just the same way if you delete a record from an access database or a simple text file then once its gone its gone, you dont expect it to be wriiten to a database and recorded and even more so you dont expect that when you delete it and back up your phone it is then stored in a hard to find file on your computer.
Please tell me what other system works the same way that when you think you permantly delete something and then do a backup and find the deleted records are then stored in a backup, why would you want that? you have already specified that you dont want it by deleting it so why make a copy in a backup?
Ontop of that Apple have already stated that imessage is so secure using end to end encryption that they cannot give law enforcement a copy becuase they dont have it but then then they store the contents in plain text on the phone after the user has deleted it! how secure and private is that?
So yes, Apple are knowing keeping a copy of all sms/imessage and call records for some reason and I can be sure its not for the users convinience.