The auto-replies (out of office responses) will be considered as replies affecting SLA calculation and performance metrics related to the ticket. To avoid that, set up an automation rule (under Admin > Workflows > Automations > Ticket updates > New rule) to close the tickets automatically when these auto-responses come through.

When an action performed by: 


Involves any of these events

Reply is sent

On tickets with these properties: 

In Tickets > If Last Interactions > Contains > Out Of Office, Unavailable

Perform these actions

Set Status as > Closed