Does an unfounded or closed CAS investigation still get referenced in a later parenting dispute?

It can be, even though it wasn't substantiated. An unfounded or closed investigation doesn't disappear from the record entirely, and either parent can raise its existence in a later parenting dispute - for example, to argue a pattern of concerns over time, or, from the other side, to show that repeated investigations have never turned up anything. How much weight it carries depends heavily on context: a single unfounded report years earlier with no other history behind it is generally treated very differently from multiple reports, even unfounded ones, that form part of a larger pattern a court is being asked to consider.

Courts are generally careful not to treat an unfounded investigation as proof of anything on its own, precisely because "unfounded" means a concern was raised but wasn't substantiated - it isn't the same as a finding that the report was false or made in bad faith. If an old, unfounded investigation is being raised against you in a current case, your lawyer can help put it in context: explain what it was about, note that it wasn't substantiated, and focus the court on the current, relevant evidence rather than letting a historical, resolved matter dominate the analysis.