I very much doubt we'll learn his name. The question "Doctor who?" is likely more about the type of person he is or something he did in the past, something to do with the very nature of his character. At this point, giving him a name would just be odd.
Yes, I think it relates to the kind of person he is. The Doctor has at times answered the question "Doctor Who?" by saying that he is the last time lord with all the rights and authority to right wrongs, even destroy entire armies. It would make sense that groups like the Silence would be afraid if the Doctor answered the question that way which is why they tried to kill him in the first place. They don't want him to answer the question because it would mean their demise.