The easiest way to hide 12 years of weapons building is to bury if you happen reside in a big-arsed sandbox. The Iranians are reported to have literally underground weapons centres; why not the same scenario for Iraq?
The Manhatten Project was able to maintain absolute secrecy for years to the extent that the Truman didn't even know anything about it until FDR died, and that was all done without Saddam's ever-present threats of the worst tortures imaginable.