If the owner doesn't bring it up in a couple days and the awkwardness persists, I might be tempted to go right to him and say, "look this is awkward because I'm new here and I don't know anybody really, but I think I saw a couple having sex in your office a few days ago when I stayed late. I didn't get a good view of them of course but I thought you might want to know since they must have been employees and that seems really disrespectful of you." At that point he has no choice but to thank you for telling him, apologize that you saw that, and promise to do what's necessary to keep it from happening again.

You will probably both know you both know at that point but at least you will both know you both know you both know and you both know that you're leaving it in the boss's court. I don't know that the stage business with the glasses is really even necessary.