You all bring up great points. I had completely forgotten about the poison scene where masks of the waif and Jaqan were both used. So this leads us to one of two conclusion I think. 

 

1. They can use magic (or something of the like) in lieu of physical faces when they want to. This does not pass muster for me. If that was the case why do they need the hall of faces?

 

2. The waif and Jaqan are dead as Jaqan says he is and whoever these two are have been wearing faces from the hall the entire time, swapping them out as needed to mess with Aria. 

---