When you create Shared Services provider in your SharePoint Farm and want to assign already existing app pool make sure that the name of this application pool is exactly the same as SSP name. If the name is not the same then Sharepoint will create new app pool with SSP name even though the new SSP will use the app pool that you assign to it. Why I think it's important is the amount of app pools will directly impact the performance of system.
Just examine you IIS and delete this unused app. pool.