My 2¢:
If upgrading the deb packages does *not* restart the services, then you can just upgrade all the slurm packages on the controller, then restart slurmdbd first and slurmctld afterwards. (This is how I do upgrades with rpms.) If upgrading *does* restart the services, then you'd have to stop and disable them first (stop slurmctld, then slurmdbd), and after the upgrade, enable and start them (slurmdbd first), as others have answered.