Barring volcano lair level evil or some fear that they'll get bomb trucked if they're on the runway too long, there's no reason to just leave that space empty. So really, the question should be what else are they loading up, and if not in Kabul, then where. It wouldn't be arms, that ships sailed and the PR of prioritizing guns over people would go over 10x worse than the PR of losing more guns. I can't imagine its sensitive intel. Not because such intel couldn't exist, but that its unlikely to be mass planeloads of it without press on the ground noticing.
Really, any press on the ground should have caught large quantities of anything taking up that space and reported on it like mad, which brings back to "its probably actually full of people". I don't know where you are getting the passenger load numbers from, but unless its from filming loading up and flying off, I'd suspect they're falsified. Its not like the US or other countries would feel the need to lie about how many afghans and the like they're running out, they get hard at the thought of the PR of being able to tout more of them. So it stands to reason there's some other reason to keep them secret. Something worth risking American lives over.
Mostly just thinking out loud here, I'm on the edge of believing it really is just volcano lair evil afoot.