All Query Activities from DESelect Segment are running inside Salesforce Marketing Cloud via API.

A Query Activity created and started within DESelect Segment will take the same amount of time to run as the same Query created and started in Automation Studio.

In case you find that DESelect Segment Selections are taking a longer time to complete than a corresponding Query Activity in Automation Studio/Journey Builder, here are a few points to look at:

• In case you make changes that you want to include, always run your DESelect Segment Selection before using the corresponding Query Activity from Automation Studio.
• Check for Prio Deduplication on your DESelect Segment Selection. If this feature has been applied, 2 Query Activities will be generated. The first Query Activity will correspond to the normal Selection and the second Query Activity is where the Prio Deduplication applies. Make sure to include both Query Activities.
• Make sure you are using the correct Query Activity.

Related Article: Using DESelect Segment Query Activities in Automations/Journey Builder. 

How does DESelect Segment handle deleted Selections' Query Activities in Automation Studio?