They are actually. iCloud backup stores the messages by default. If you go and set Messages to use iCloud sync, then they're synced end to end encrypted. Apple

They are actually. iCloud backup stores the messages by default. If you go and set Messages to use iCloud sync, then they're synced end to end encrypted. Apple then removes the messages from the iCloud backup, and instead stores a backup of the end to end encryption key for Messages. If you want your messages to be truly inaccessible to Apple / agencies with warrants (and also unrecoverable after losing end to end encryption access), then you have to turn off iCloud backup. Apple's documentation needs to be a little clearer on this but the system is basically designed with the accurate notion that the biggest footgun for 90% of users is not "the government was able to access my messages with a warrant" but rather "I lost access to my end to end encrypted messages".