Unarmed F-16 -- why would it happen?
If the article is to be believed, the gun was probably loaded with M55A1 training rounds which are a steel core projectile with an aluminum nose-cap used for target practice as opposed to the M56 HEI or M53 API rounds which the jet would go to war with.  If it had either a full or partial magazine of the M55 ammunition, it would have had at least some firepower available to it, but I imagine the crew had resolved themselves to, if necessary to protect Washington DC, ramming their aircraft into the jetliner.  It just goes to show you how utterly unprepared this nation was for that kind of a ruse.  Its obvious that this was an anomalous and desperate measure by two very brave ANG pilots who responded to a call using whatever resources were available to them.

Post 9/11 most fighter bases in the nation keep at least two birds housed in a Hardened Aircraft Shelter (HAS) in a 'hot' condition, that is, fully fueled, 520 rounds, 2 x AIM-9s, 2 x AIM-120s, with the INS aligned and two pilots keeping watch round the clock for the alert.