Don't encode your themes or plugins etc. Its crap especially with themes. It also prevents people from helping you to improve the product.
Protecting themes that way creates more hassle for the consumer than its worth.
It also makes it harder to debug etc.

If you want to protect in a basic way you make the theme contact your site upon activation. It will only activate if the domain used is registered with your site.
This way you can also provide automatic updates to the theme itself.

I would recommend however that you start out by selling themes on themeforrest and similar sites. Also make some free themes so people know what you can do before hand.