If Daniel has nyctophobia,,,

[MrWhitticus]

Just wanted to note that Daniel had nyctophobia all the way back when he was a small child. It can be read in the loading screens; his father urges him to go into the basement, he accidentally breaks a jar of paint and he cries and knows he will be punished.

The loading screen actually read:
"[Daniel] wasn't particularly afraid of the dark, but he had always disliked going into the basement."

So he possibly didn't have the phobia by this point, and the event in the tomb spurred it on or one of the other theories that you guys came up with.