Snakes getting inside coup?

[M SILKY BANTAMS]

So our silkies have hatched 2 cute little chicks.Last weekend my husband said another brand new one was under the mother. So I've been keeping an eye out for the third one. So yesterday I got all the mothers up BC they share 2 beds and all my silkies are mothering the eggs together. However, there was no other baby. I thought my husband picked up some big chicken poop. But last night I told him my theory and he said no it was a baby chick.
So today I go to see the two babies and only one is up and about. I thought surely the other one is under a mom. Nope. It's gone!! Without a trace.
I checked all along the fence and there is no holes. However at the top of the roof the rain has serperated it from the house.
So at this point I'm either thinking a snake is coming in at night and eating the babies. Or my 4 lbs Pomeranian is climbing into the coup and eating the babies whole.
Super sad I'm down to only one chick

 

[chickenweirdo1]

So sad. I would say put some netting or poultry wire over the whole.