Are there any natural methods of preventing an omphalocele?

None Known. An omphalocele is a birth defect occuring prior to birth. The triggers are unknown asis prevention. So no.
No. Omphalocele is a sporadically occurring abdominal wall defect. Intestine and often liver herniate into the umbilical cord. Surgery can be undertaken shortly after birth to place the abdominal organs into the abdominal cavity and close/repair the abdominal musculature.