I note your top screenshot shows Reopen Last Closed Window as Control-Shift-S, too, which certainly suggests something is amiss with your setup. I don't think it's on Apple's end, as that command, when relevant, shows up in the History menu for me as Shift-Command-T, as expected.
It might be worth disabling your third-party stuff if possible, or booting into Safe Mode, to see if there's some kind of conflict going on. (It's not too hard to imagine that something's different in Safari 10 which doesn't play nice with previously compatible software.)
