Piping in... same issue last night, I ended up removing my Apple ID from Messages on my Mac, removed Messages from the notification center completely in System Preferences, restarted, re-enabled everything, and it went back to normal.
Makes me wonder if it was server-side or something with my computer... if others had the same issue, then it could possibly be server-side (although that doesn't make sense, because I don't think notifications are based on servers, just notifying what the app says, in this case Messages, which DID get the messages)... really weird. iCloud tabs were also not syncing too, which leads me to think something was going wonky last night.
But, yeah, do try what I did. If all fails, try another user account and see if the problem persists. Annoying, I know, but I guess that's part of dealing with a 10.x.0 release.