I think you live in an area that has very large hawks (like Goshawks) who will eat ducks, but they usually eat them on the spot and don't carry them away. A coyote might carry them away, but you said it would be very hard to get in your yard other than from above. I'm not sure about an owl as they often can't carry off something like a duck.
Cats, like bobcats, can climb 6 feet fences, I've seen them do it, too. And, they live in very urban areas right under people's noses. You wouldn't even know they were there most of the time.
I would get your remaining duck a companion, but I don't think she'll get depressed without one. It's just fun having two ducks around.