You can use affiliate links after the fact. You don’t have to decide upon building a WordPress site that you’re going to optimize it with Amazon affiliate links. You can decide down the road that you want to give affiliate marketing a try and, consequently, revisit old content, embed affiliate links within it, and start generating revenue that way--especially if your old content is finally starting to take off.
I recognize that the list above is short; however, that’s because Amazon affiliate marketing really doesn’t require a specialized theme in order for it to work well (unless it’s one of the unique cases noted in the themes above). Instead, you’re better off using WooCommerce if you want to build a full affiliate store or simply stick to the WordPress theme you currently have and add affiliate plugins to the mix.