Yes, End listing done automatically. When a product deleted or inactive in shopify then the corresponding mapped/linked item will be end listed automatically.   

To do End listing item automatically,  Plase navigate to Sidebar Menu and click on Settings. In Settings page click on “Inventory Sync". This will open inventory section as shown below   

In this section, check “Yes” at “Enable Shopify Inventory Sync” for inventory sync from shopify to ebay.    

Select “Unpublish from store” from the dropdown at “On Product delete/inactive”. This setting will end listing on eBay when shopify product deleted or inactive.