They normally ship in heavy plastic bags. There is a little water vapor transmission, but not enough to seriously degrade the Ammonium Nitrate - except for tears/punctures etc.
One press release commented about damaged cargo. My guess is the local terrorists used it as an explosives bank. Being a customs port, it should all the watched/counted, but beirut is one of the most corrupt countries on earth = easy to steal/import anything. Now you know how Hezbollah gats their stuff, as I am sure Israel knows and monitors well.