My nonD son had a regular belly button (inee) and developed a herniated bellybutton about a week after his stump fell off. They just let it go and it is still an outie. They check it pretty regularly at his pediatricians and so far no problems. He may eventually need surgery should it get worse. No thyroid problems at all. He's 14 now. Hopefully that will be the case with your little guy too!
Mom to Tim, 20 dx'd at age 2 1/2, started omnipod 4/11/2011, previously MM for 6 years. Dexcom currently as well.
Natalie, 24 nonD
Brady, 18 nonD