I just poked around for a few minutes looking at the css grid he used for making it. It's interesting stuff. I think that what the newspaper layout does is make the newspaper readable while you walk by, over someone's shoulder, from various distances, etc.
These are newspaper problems. They don't exist when you're reading a screen. Novels or magazines aren't formatted this way. Why should sites be? It's not about content. It's about how/when you read it.
That said, I have learned something about how to layout a page in a way that looks like news. I suspect the main value of this is creating a mental association with a newspaper.
Sure. The filtering may be added value though it feels like it goes against the concept to me. The newspaper snapshot is almost a representation of the zeitgeist. Using those associations and filtering at the same time seems almost like propaganda.
I find Hacker Newspaper uglier and less legible, because it's non-linear and harder to visually scan/skim through the items. However, as a non-linear format, it is inferior in design to newsmap: http://newsmap.jp/#/t/us/view/