Hi guys,
The setting found at My Settings > Auto-Responder > Options tab > "Limit responses to once daily" is still available in SmarterMail. However, it will not show if the domain has been enabled to "Restrict auto-responders to once per day per sender." This is found on the Technical tab when you edit a domain as the System Administrator. Can you check the domain setting to see if it's enabled? If so, that explains why the setting is missing on the user level.
Thanks!