I rarely use Safari on macOS, so let me be sure I'm understanding what settings you're referring to. You say you "explicitly set" YouTube, etc. to "deny" in Safari, but I don't see any such setting. All I see is which websites to allow notifications from (Safari > Settings > Websites > Notifications ("These websites have asked for permission to show alerts in Notification Center"). So are you saying, for example, YouTube is not in this list, yet you're still receiving notifications in Notification Center from YouTube.com?