>It looks non-functional and ugly to me.
Non-functional and ugly? I'd say this is subjective, but I find this assessment objectively wrong.
It's complete accessible, and totally functional for what it does -- present a series of sections and display code examples. And it's also quite obviously well designed from an aesthetic perspective.
(There's no black box in the actual site in Chrome, but even with the black box, it's a totally fine functional design).
As for the NYT, it looks like a compromise between looking like a print newspaper of yore, a portal of slightly less yore, and a modern news website cramming everything in the same start page.