1) Well-intentioned people in different branches of government and/or CIA vs. WH have different ideas as to the impact of information. For ex., in Afghanistan, the CIA's line was "we couldn't be involved," even though we were obviously involved. Thus the charade of all weapons being Soviet or East Bloc that were "captured" had to be maintained until 1986 when Casey finally approved the Stingers.
One group favored a "slow bleed" and thought that if we didn't push the Soviets to the point that they actually increased their troop involvement and won the war, we would be able to slowly tear them apart. This was the official Reagan strategy, because they were focused on building up the strategic assets, on economic war, and on the Contras.
The second group, led by CIA rouge insiders, Charlie Wilson, and several influential civilians, sought to "win." They tried to push the CIA to get more involved. But the CIA desperately feared that too much American involvement would result in the Soviets simply moving on Pakistan and/or getting India to do it, with Russia's support. So you can see the validity of their concerns.
At its peak, the operations involved SAUDIA ARABIA matching all U.S. spending for the muj on ISRAELI designed and built weapons (which were used as long as there were no Stars of David on them), as well as CHINESE provided weapons, all of which were funneled through PAKISTAN without a single identifying American mark on them!!!
2) What comes out is that there are very good reasons for keeping things secret. Gust Avrakodos, Wilson's partner-in-crime, thought that he as a spy was at his best when he accomplished his mission and the press was convinced he had failed. Therefore, "bad press" for CIA operations was often an indicator that, in fact, they had achieved all their goals.
One could therefore conceive of any number of reasons not to publicize that the WMDs were spirited away with, say, RUSSIAN, FRENCH, or GERMAN assistance under the agreement that the SYRIANS would lock them up or destroy them. Perhaps Syria reneged; perhaps the Israelis just learned of the agreement; perhaps they decided they couldn't trust Syria; perhaps the French or Germans suddenly "gave permission" to take them out . . . .
I have to admit that I am fairly skeptical of this story. It reminds me to much of the stories from the Balkan’s where we found no mass graves and therefore stated that the bodies must have been moved (since we obviously couldn’t have been wrong about the massacres in the first place /s). So, unless I see hard evidence that WMD’s were moved to Syria then I see no reason to give this story much credibility.