why do I always have to reboot in order to apply updates? May I just shutdown in fedora atomic?
rpm-ostree staged deployments are finalized during shutdown, so shutting down is equally effective. The next boot will use the new deployment.
AFAIK, once the software is fully updated the shutdown and later restart is effectively the same as an immediate reboot. This should be the same regardless of the OS type – standard linux or ostree based.