I just completed several tests and latest findings are:
CCC will clone to a drive formatted MacOS Extended (journaled, Encrypted)
That clone is bootable
The password to the encrypted clone must be stored in a private keychain so CCC can locate it if automatic clones are to be made.
Disk Utility has some errors in displaying the relationship of volumes on a drive when one of those voumes is encrypted.
System Report cannot discern what partition table is used on APFS formatted drives
I just got a notification that a new iOS 11 and Mac OS 10.13 have been released, but they have not appeared in App Store yet. I will forego further testing until I actually get the new betas. My prime hopes for the new betas are...
iOS 11 — fix whatever is binge eating the battery in my iPhone. (I strongly suspect it is the cellular module)
MacOS 10.13 — fix whatever is causing my RAID array to kernel panic the system
If we knew what it was we were doing, it wouldn't be called research, would it?