If you listen to interviews with Honnold, he’s very clear about the fact that he still feels fear. If you watch the clip of his first free solo of Half Dome, you can even see him have a little freakout moment standing on one of the ledges during the climb.

The only abnormal thing about his brain scan was that his amygdala activated less than usual when he looked at frightening or disturbing images, which would be entirely compatible with deliberate desensitization (perhaps through ~20 years of practicing climbing with no protection?)