Unfortunately, it seems as the pop-up functionality is not given priority by the product development department. It's got such a great potential, but the fact that it lacks so many basic features, and has beeing so since it's arrival in HubSpot, is kinda frustrating..
Hidden fields in pop-up forms should be standard functionality. Even with Marketing Enterprise the only solution is creating a workflow, which should be absolutely unnecessary. This is error prone and a waste of time. I hope HubSpot will fix this in the near future.