ooh, it's very nice!
Is there anything underneath? I know rats can burrow. They can also climb up to where your wire gets wider (cattle panels). I'm not saying you have rats but I do think they like to grab 'food' and take it back to their nest or somewhere else they feel safe, and then would...
Could the peeping you're hearing be coming from inside the eggs? not that that would explain what happened to the other eggs and any ducklings that may have hatched from them.
Oh, I was
hoping you were going to say something that meant she could just be really good at hiding them!
Could you take the remaining eggs and keep them warm enough until they hatch?