I am inclined to think they were not aware it was out of service.
There is an important difference, between knowing it was out of service (logical level) and being aware that it would simply not be there (subconsious level). They probably knew it was out of service, their subconsious expectation however was that it still would be visible, which it probably was not. They were very well aware, that they had to use the right of the two runways, they were not aware that what they saw were 28R and Taxiway C, and not 28L and 28R.
The circadian time seems probably very important
Definitely. The more tired you are, the less you think and the more you act intuitively.