Actually the embedded reporter said that they never checked the cache, so they didn't know if there were weapons still in there or not.
"There wasn't a search. The mission that the brigade had was to get to Baghdad. That was more of a pit stop there for us. And, you know, the searching, I mean certainly some of the soldiers head off on their own, looked through the bunkers just to look at the vast amount of ordnance lying around. But as far as we could tell, there was no move to secure the weapons, nothing to keep looters away."
So troops didn't find the facility empty.