Yes, I've written my own HN reader as well as other apps using iframes...and basically the situation sucks.
With a reader like this, you have two real options: * Include regular iframes and risk an increasing number of sites opting out with JavaScript or (more politely) an X-Frame-Options header. * Use <iframe sandbox> to prevent people busting out of it with JavaScript. But that stops all JavaScript, so apps and videos won't show up.
Pity. iFrames have so many great uses like this Reader. Browsers really need to deal with the clickjacking problem instead of forcing everyone to bust out of them and making sites like this unusable.