Upvote arrows blend with white instead of transparent, giving a weird look.
The orange goes well with black.
Not all users might want #000, but for OLEDs it's gorgeous.
The @media selector requires a OS/Browser support, to extend that a simple way is programatically add a .dark class to <body> (edit: based on a checkbox in their profile), and add selectors with .dark.
Some colours on the site are hardcoded, like the orange asterisk on your own comments, and newbie green. They both go fine with #000 imo.
Edit: tested on the other pages, looks good imo. Login/logout don't have CSS, which'd be a bit jarring.
It's a bit sad there's no distinction between the #hnmain and the background anymore, I think if that were desirable I'd probably change <body> to #111 or so.