If you have tinnitus issues, I would recommend Masked. Ultrasonic usually gives me tinnitus so I avoid using it.
Plus, if you are using Ultrasonic, you need to follow certain precautions regarding its volume to get it right. Masked track not as much.
Other than that, both files have the exact same information. In the old days, ultrasonic was useful since the older versions of the subliminals were much longer and/or had to be run for a long duration (at one point running subs for 8 hours a day) for which ultrasonic was useful since it could be played on a speaker.
But now since we only need to run one loop of a 15 minute loop every other day, Masked makes more sense. And with some running microloops that is between 30 seconds to around 7 minutes), more people opt for Masked right now.