No, only 100% of the account funds needs to be reported. The funds are jointly owned. I am unfamiliar with financial aid documents, but so long as the total value of the account is reported OP should be okay. Doesn’t seem that custody is relevant as assets of both parents & of the student would be relevant for any decision regarding financial aid.
Again, I am not familiar with the financial aid forms, but it seems only fair & reasonable that assets of both parents are considered whether currently a custodial parent or not.