They actually built a fake building around the reactor, in order to avoid detection. And, apparently, it worked.
Until Israel demolished it via an air raid, last September.
Mohammed El Baradei, Director General of the IAEA, when reached for comment, said through mouthfuls of foie gras at a conference in Manhattan: “We really had no idea about the Syrian reactor. It’s hard, you know, when they won’t just be honest with us, and admit what they’re doing. Also, we like to stick to big cities and buy expensive stuff on the U.N. dime, rather than travel to icky places like eastern Syria, where our pants lose their creases. Although, they buy us nice stuff, too! Pass the Champagne, please.”