While there maybe encryption in transit of messages, the encryption of messages at test is effectively defeated when the messages are at rest in icloud.
I am curious, is it possible to do an icloud equivalent backup without using icloud? Perhaps with a different backup app, nas, etc?
Ideally it would be nice if you could opt yourself out of having any conversations backed up, but I'm sure to Apple the privacy benefits doesn't outweigh the amount of customer support hours that would be wasted explaining to people why some of their conversations aren't transferring to their new iPhone.
ISTR that local backups would contain more than the icloud backups as well - there are some things that won't be backed up into the cloud?
itunes.