your notifications, those notifications are gone. The messages themselves are still there, but the little notice that says you have a new message is gone. So if my wife was checking my messages before I saw them, I wouldn't see the notification.
You'd have to have a rule saying that you can look only at each other's old stuff, but not the new. But for anyone who is this concerned about this stuff - people who apparently don't trust each other - that rule probably wouldn't work either... b/c they don't trust each other.
So, my advice is to quit worrying about it and learn to trust each other. If your spouse is going to cheat on you, it's not going to be because of facebook.