Although you can't delete images uploaded to our server, you can overwrite them with a blank dummy file, as you described.
For the logo/header image that appears on the top of all your Marketplace shop pages, E-junkie thank-you pages, and PayPal checkout pages, go to Seller Admin > Edit Profile > Upload Your Logo.
For images uploaded for a specific product's Marketplace shop listing, go to Seller Admin > "List Products in your E-junkie shop and our Marketplace" > Select a product and click "Add/Edit Listing in E-junkie shop and Marketplace" > Click Next and Submit until you see the Upload Images button.