Removing the Shopify Marketplace Connect files from the Shopify theme usually isn't required as they have no impact on websites. However, if you want to remove this can easily be done:
Go to Sales Channels > Online Store > Themes > Customize > Edit Code
Open 'Snippets' > delete 'ebay-default.liquid' and confirm
Open 'Assets' > delete 'ebay-bootstrap.css' and 'ebay-styles.css' and confirm.
For further assistance, please reach out to marketplace-connect@shopify.com