this article is talking about UIs, and more specifically user-interaction driven interfaces. it shouldn't be relevant to SEO at all, because it concerns what happens after the page loads, not the initial page load (which is what the search engine sees)
A nice solution here is to have a 'traditional' application with new page loads for links, so that search engines can follow them. You then enrich this application with Javascript, placing click handlers on the links to replace their default action (loading a new page) with a similar action performed through Javascript/AJAX.
