Generally you only use RequireJS in its loading form during development. Once the site is done and ready for deployment, you minify the code. The advantage here is RequireJS knows exactly what your dependencies are, and thus can easily minify the code in the correct order. Here is what it says on the RequireJS website:
Once you are finished doing development and want to deploy your code for your end users, you can use the optimizer to combine the JavaScript files together and minify it. In the example above, it can combine main.js and helper/util.js into one file and minify the result.