People seem to assume his eyes were damaged but there is actually shit going on with Miller that not enough people are paying enough attention to.
When you rescue him his eyes are yellow but still fairly normal, I've been trying to figure out when the change occurs, I'm pretty confident it's right after he gets back to Motherbase, maybe it's when you get Quiet, for some reason he can detect Quiet's presence and seems to see her as a threat despite everyone telling him to relax, I'm pretty sure his eyes are always changed once he has the coat/beret regardless of whether it's a Quiet cutscene or Huey's torture.
When you compare his eyes to Code Talker and The Skulls, they are exactly the same, if you combine that with Code Talker's warning he received from the parasites, it seems pretty clear Miller is up to something or that he is hiding something from you, I'm pretty sure he has some sort of Parasite power, but I have no idea what, his blindness is inconsistent so I think he can sense living bodies around him and stuff like that, probably much like Quiet.
If you kill Quiet and play without her, Skullface still tells you that the English strain is close to you, but Quiet was told by Skullface that she has the strain, so that's why she never tries to talk.
Miller was ambushed by the Skulls and miraculously left alive for a reason...
That moment I wonder if he made a secret deal with Skullface, hence DD containers at OKBZero.