1) You are too kind.

2) We see Cillian Murphy go from clothed to naked before the board investigating his security clearance, not merely because his personal life is being discussed, but because of how nakedly vulnerable he was with Jean Tatlock (that part of the story hit me hard, emotionally). Then of course, we see from his wife's point of view, the imagined spectacle of Oppenheimer and Jean having sex, in front of them all. This is intended to show her embarrassment at having private matters paraded in front of everyone else. She already knew about the affair, but having it dredged up in this context and "spoken to history" is upsetting. This visualises her feelings in a powerful way, and works well, I think, in conjunction with the other hallucinatory material seen in the second half of the film (for example, Oppenheimer's guilt-induced horrific nuclear hallucinations).

Sorry for going into film critic mode in the comments, but you sort of asked for it. ;)