Yes they're end-to-end encrypted (according to the release notes here https://support.apple.com/en-us/HT208067#114):

- Store your messages, photos, and other attachments in iCloud and free up space on your devices

- All your messages appear when you sign into a new device with the same iMessage account

- When you delete messages and conversations they are instantly removed from all your devices

- Your conversations continue to be end-to-end encrypted

This Messages in iCloud support article has more details on how to set it up: https://support.apple.com/en-us/HT208532