You can use Throttling while creating Scheduled Alert but this will trigger multiple alert for multiple output in single scheduled search window.
Please follow below steps while creating scheduled search (Alert).
1.) In Trigger Conditions, select Trigger for Each Result
2.) Then tick the Throttle.
3.) In Suppress results containing field value, please provide field name. If you are counting using stats command then give count in this textbox.
4.) Suppress triggering for -> Here you can give time period till that splunk will not trigger an alert if count will be same (I am assuming that you are using stats count in your query).