... unless it's iOS 6 and you try to use the 'open in a new window' links (javascript window.open with a target of _blank) for the articles.
When pinned as a Web Clip, the site opens up fullscreen and addressbar-less and without tabs / as a single window. The attempts to 'open in a new window' just replace the HN mobile view altogether with the article and then strand you there without gestures or controls to move Back.
How do you return to the HN UI after clicking a story when there isn't any browser chrome / back button? That is the only downside that I have seen from adding it to the home screen.
Previously discussed: https://news.ycombinator.com/item?id=6178534