Yes, this is all very strange. It depends on whether there is any pattern to the nature or tone of the 'missing' texts . That is, were all of the missing texts incriminating/sensitive, or were they random.
If they were all sensitive in nature then that would imply some intelligent force behind them ending up in the plaintext 'database'.
In that case, like you say, it could be some hidden feature that keeps a copy of any text that is deleted. One would think though, that if the ESOC set out to collect the text messages, they would anticipate texts being deleted and already have a feature like that.
If the content seemed mostly random, then the text database could just be some failsafe in the programming that dumps data there in the case there is some problem putting in the normal database. (if you're learning to code, you should take note kek).