zfs_enable="YES" set. This was after the reboot following the first freebsd-update install, but before I ran the second freebsd-update install.That did the trick. I guess I hadn't actually finished installing yet.I've just finished updating from 12.2-RELEASE-p6 to 13.0-RELEASE using freebsd-update() and had the same problem. I hadzfs_enable="YES"set. This was after the reboot following the firstfreebsd-update install, but before I ran the secondfreebsd-update install.
I manually imported my two missing non-root pools, which succeeded fine, then after another reboot they were found automatically on boot.