If you have Messages in iCloud enabled, it's not included in your iCloud backup. See footnote 2 in the support article below.
"2. When you use Messages in iCloud or turn on iCloud Photos, your content is automatically stored in iCloud. That means that they're not included in your iCloud Backup."
As you probably know, when you look at iCloud > Manage Account Storage > Backups > [your phone] > Show All Apps, you can see what's included in the backup and whether any apps got disabled.