I have fake eggs in all the nests and still get punctured eggs almost always on the end where the air pocket is. Why? They also break eggs. They move the straw from the center of the box. We have tote lids on the bottom of the boxes. Should I get mats or maybe add shavings?Well at least congrats on the double-yolker!
Perhaps once the shellless eggs stop, they'll leave them alone. The holes might have been made by their toe nails even.
One idea some do is put curtains on the nest boxes. If that doesn't do it, my idea was to paint the inside of the nest boxes black, then hang the curtains. They can't eat what they can't see.
Another idea I'd heard of was blowing out an egg and filling it with mustard and putting it back in the nest. Or, putting plastic or wooden eggs in the nests.