So there is an option to ignore files in jshint, but it’s not set within .jshintrc but rather a separate file .jshintignore, which makes sense. However, while jshint will look for .jshintrc in your project’s subdirectories, .jshintignore needs to be in the project root. So with Twitter Bootstrap, .jshintrc is in /js while .jshintignore needs to be placed in /.
So to solve the problem in my question /.jshintignore needs to contain:
js/html5.js
js/theme-customizer.js
And that’s it!