If you were selling directly from your own site, you'd simply set up two versions of your product, one with and one without Shipping enabled, and the Shipping-enabled one could even use the "Bundle other products" feature to issue a download link for the file already uploaded to the download-only version.
However, I gather eBay requires you to offer shipment of a physical hardcopy in order to sell downloads at all, and you want to give your eBay buyers the option to waive delivery of that hardcopy? Unfortunately, we don't have any built-in way to accomplish that with eBay sales. In this case, the IPN we receive from PayPal is our first indication of the order having been placed, at which point we process the order and log the order details immediately, so there's no chance for the buyer to state a hardcopy preference before or after that could get stored in your Transaction Log.
You might consider customizing your E-junkie-generated thank-you pages where we provide the buyer's download link, and/or the thank-you email message we send with a link to that page, to add instructions for buyers to specify whether they want a hardcopy mailed -- e.g., this could be as simple as providing your email address where they can contact you to state their preference.
I can think of some more sophisticated approaches, but setting these up would require some advanced Web development skills, such as setting up form handler scripts or programming other custom scripts; let me know if you're familiar with that sort of thing and want further pointers along these lines.