When you delete the Service applications, their Application Pools will not get deleted - They'll become orphan/unused. So later when you create a new service application with same application pool, SharePoint will throw an error message: Application pool is already in use!
In another case: An application pool already exists with the name specified
So, How to delete the unused application pool? From IIS? Nope. IIS will not provide the interface for managing service application's application pools. But we can delete service application's application pool in SharePoint 2010 using powershell.
Use these below cmd-let to get list of service application's application pools.
SharePoint 2010 delete orphaned application pool: To delete a application pool of service application, use the cmdlet:
E.g. Remove-SPServiceApplicationPool -Identity <Orphaned Application Pool Name>
Get-SPServiceApplicationPool -Identity "name of the app pool" | Remove-SPServiceApplicationPool
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