They removed it in Sierra. I've sent them a comment in their Suggestions site before, unfortunately nothing has changed. Night Shift, however, is a good compromise for me and I don't mind it as much anymore.
Would it be nice if they included a Notifications Center that was dark to match the dark menu bar and Dock? Absolutely, I'd love it.
Am I going to go and berate Apple for not including one? No.
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That is a good thing. If every segment of customers all got their way when it comes to "aesthetics", then Apple products would be a jumbled mess. Don't over estimate how important a few thousand people on internet forums are when it comes to this stuff. I wouldn't be surprised if 90 percent of Mac users have no clue you can change the colors of the menu bar and dock as is.
This I completely agree with. While I think having Notification Center match the user bar and Dock when set to dark would be nice, I'm not going to berate Apple too much for it. From my experience, the majority of Mac users don't even know the option to use a dark menu bar and Dock exists. Having a unified "dark mode" would take an incredible amount of work and I can imagine how horrible some apps would look in it.