My thoughts not backed by research Normally when ducklings are still following Mom the mom is not laying eggs. Since Mom is laying it gives a behavior to mimic that most ducklings don't experience.
It is actually normal for hens to get up while the first pips are happening. No reason to think they are shrink wrapped. (Incubator eggs are in a human altered environment that makes them slightly more susceptible to shrink wrapping)
This could go either way. I have fairly large duck flocks. The majority of my ducks wander most of our ten acres and return to a pen each night. One set wondered off our 10 acre property and insist on staying at the neighbors pond. Another set decided to be part of our Silkie coop. This...
You say you see a shadow. That is how some describe seeing an internal pip. Usually you can see the ducklings move at that stage. Dark room with cell phone flash light shined through the air cell is how I candle eggs.
You mentioned maybe more space, What space are they in now?
You say they are keeping you up at night. Is there another option that keeps them farther from your bedroom?
Also what exactly are you feeding them?
Anytime a duck has eye issues make sure the duck has clean (at least before the first dunk) water deep enough for head dunking. I don't think this looks like a problem. I can't tell from the picture if it is coloring or possibly thinner feathers around the eye.
Americana (EE with traits similar to Ameraucana)do not fly any more than other chickens. There is no standard, so traits and personalities may vary more than breeds with standards.
The simple answer is yes they can still hatch. How long have there been twelve eggs? How many days has she been sitting part time? Many ducks when they first go broody don't sit 23 hours a day, but later become more committed.
It will not develop angel wing due to feeding 20% protein. I don't know about Muzuri's starter as far as other details. The feed I use is designed for all stages of life.