My son goes to school in NJ but lives in HI. He worked in both states. Does he have to pay taxes on his excess scholarship amount in HI & NJ?

He won't be taxed twice.  He'll be able to take a credit on his HI return for the taxes he pays to NJ.  Just be sure in TurboTax that you complete his non-resident state return first, before you do his home state return.  The sequence is important so that the credit flows properly.