My son was diagnosed with an omphalocele at 12 weeks gestation. It is my understanding that an omphalocele is a herniation but NOT an opening. My son's liver herniated through the abdominal wall into the umbilical cord. Calling it a hernia is also probably inaccurate as its not a rip, rather a defect in the formation of the abdominal wall. I was subject to a level II ultrasound which is essentially a more intense look at the other organs of the baby, searching for other possible defects such as heart defects as you mention. My son did have a hole in his heart early on in the pregnancy which had resolved itself by a later ultrasound. My pregnancy was monitored to the very end. A C-section was scheduled to avoid damaging my son's liver in the birth canal. He was operated on within 7 hours of birth. He will be celebrating his 8th birthday in about 2 weeks. By the way, we refused the amnio because down's syndrome and trisomy 18 don't usually correlate with omphaloceles.
What you describe for your sister's pregnancy sounds like gastroschesis where the intestines float out through an opening in the baby's abdomen. I don't know as much about this defect. Has she asked about in-utero surgery to push the intestines back in and repair the opening? If there's a hole in the heart, if it doesn't resolve, could it be repaired with surgery after the baby is born? What is the ultimate prognosis for the baby if there is another defect?
I am so sorry that your sister and you have to deal with this. I truly hope, with the miracle of modern medicine, that it all turns out well.