It strikes me as a reasonable compromise. It seems pg was paying attention to the recent poll, where quite a few HN readers expressed support for HN joining in the blackout, but where there were some good arguments for
not blacking out HN today. By just blacking out the logo, it provides a stark reminder of the situation to any HN readers who needed reminding, but it doesn't take the site completely offline. Makes sense, since there were some good arguments that taking a niche site like HN offline wouldn't do much good anyway.
I dunno, I'm guessing pg just decided to go for a pragmatic, but still principled, stand. <shrug />