What we know is that he was in the tail section; he would go off into the jungle for hours at a time and no one knew where he was; Libby and Cindy didn’t recall seeing him on the plane; Goodwin said “Nathan wasn’t a good person”.
So here’s the question: Was Nathan someone sent by Charles Widmore, or more generally by the Dharma Initiative? Was the purpose of having a flight that was connected with the numbers an attempt to use the numbers to get someone to the island? Was Nathan hidden on the plane somewhere, rather than a passenger with a seat?
I also wonder what makes someone a “good person” from the perspective of the Others, and of the island. The smoke monster has been described as a security system to protect the island. But it seems to manifest itself as figures from one’s past with whom one has unresolved issues. Does the monster protect the island from “bad people” by giving them therapy, as it were?
This might explain why the smoke monster killed Mr. Eko. He refused to repent of the things he had done to help his brother Yemi and others.
I’m not sure I’m entirely happy with where this line of inquiry into the show might lead, but there still might be something to it.