It's a very poorly worded sentence...
I think the diagrams they are referring to came from the 2002 report otherwise they would have left it out. This is their way of trying to say that "at the time" could mean the 90's but had to include 2002.
Yes, very ambiguous.
My guess is that it refers to the 1990's or before the first Gulf War. After invading in 1991 our intel people were shocked when they saw how far along Saddam's nuclear weapons program was. It's no secret that Iraq was close to having nukes around that time. As far as that goes, the NYT piece just seems to be restating a fairly well known fact.
The posting of these documents on the net seems fairly trivial to me too. Well, not trivial, but still nothing to get too worked up about.
I think the earlier poster had it right -- YAWN.