The only reason I can come up with as to why they weren't shot down is that the gliders were unmarked. The idea of not shooting down unmarked planes flying over your fort baffles me, could someone please explain why they weren't shot down?
The central reason why there were no major casualties from AA fire during the storming of the fortress was that Eben Emael had only two AA emplacements. Located in open emplacements around the Bloc 4 bunker, the complex had four batteries of Mitrailleuse contre avions (MICA). Each MICA consisted of four 7.65mm Maxim guns joined together in a single carriage. The open emplacements were a high priority for the German assault group and they were among the first of the complex's defenses to be attacked and neutralized. Trupp 5 commanded by Erwin Haug landed on top of the MICA positions, one glider's wing actually crashed into one of the MICA guns. Haug's soldiers managed to neutralize the rest of the emplacements by grenades and suppressing fire. Some of the MICAs did fire on Haug's gliders and one of the pilots did recall a rather tense bit between sighting the AA guns and landing.
The other German commandos who were tasked with taking the bridges were not as lucky as the Eben Emael counterparts. The Vroenhoven Bridge assault lost a glider when AA fire cut one of the glider's tow cables. The bridge assault near Kanne also landed under heavy AA fire. This not only led to higher casualties among the Germans, but also denuded them of surprise so the Belgians were able to blow up the bridge before the Germans could capture it.
These isolated examples of Belgian AA though underscore the relative paucity of AA defense compared to later developments in the war. Eben Emael's four batteries were vulnerable and had a complicated command and control that prevented prompt action. The fortress's air defenses were more passive in nature, relying upon steel-reinforced concrete to resist aerial bombardment. The MICA batteries were not really suited to prevent an aerial landing as they were clustered together, unarmoured, and, as Haug's group shows, easily neutralized. Likewise, Belgian air defense as a whole was unable to meet the task of putting up a staunch defense against a fast moving enemy like the Germans. There were not enough AA tubes nor was there any real ability to sync up those AA guns that did exist to shoot down a German invasion of Belgian air space.