Pages made by decent developers are not a mess. Certainly orders of magnitude less messy than handling all your presentation in code, mixed with business logic and controllers.

Separation of presentation and content allows for information to be accessible by everyone, indexed/readable by machines, adaptable to different displays. It's also easier to maintain (content editors can't mess with layouts) and makes many performance improvements possible.

The HN site has no special reason to use tables, it's perfectly possible to render this layout using semantic, clean markup. CSS has come a long way since 1999.