Well, without seeing the briefs, I'd have to say this is a pretty specious lawsuit. Plenty of people have the same names as persons who are wanted for crimes, or are otherwise subject to detention. The fact that John Doe might get stopped because another person named John Doe has a bench warrant out on him is not only not a violation of the constitutional right to freedom of movement, it's not anything at all but bad luck.
I suppose one legitimate problem could be that the names on the list, probably mostly Arabic, have no standardized spelling and there is not a great deal of variety in Arabic names as compared to the enormous number of surnames in the US. That being said, I still think the no-fly list would pass constitutional muster.