While you can't really stop them from copying a Hype project, you can add a speed bump. Basically, you can add code to your project that prevents the Hype project from running on another website. While this code could be removed, or the content simply copied out of the project, it is a good deterrent.
You can read about this approach here...
-- Free Hype Templates 🏗 - #36 by Photics
...and here...
-- Free Template Tuesday #9 – Tumult Hype “Lock” – Photics.com
Theoretically this basic approach can be expanded. You can add booby traps to your project. So, if your Hype project is not running on your website, it can then send an alert to you via a web beacon. (Have the JavaScript load a file that's not normally loaded.) Assuming the booby trap wasn't detected or blocked somehow, that should identify the hostile website.