The baboons seem to only really be active once Oz arrives in the land. For instance, they attacked China Town because they were celebrating the arrival of the wizard. It seems reasonable to assume that, without a pressing need to use them, the flying baboons were probably never seen with Evanora before then and any interactions were done in secret.
The scene you refer to in which Evanora sends out the baboons from the top of the tower happens immediately after the scene in which she sees through her crystal ball that Oz did not destroy Glinda's wand and he discovered that she is not wicked. At that point, time was of the essence to kill him before he gathered any opposition so it wasn't worth it to try and arrange a secret meeting.
The next scene she is in, she turned her sister Theodora evil and after that point never even tried to pretend that she was good. So as long as Evanora was able to keep Theodora from seeing that she was dealing with the flying baboons, she'd be fine.
So it seems reasonable to conclude that nobody found out because she pretended to be a good witch serving as royal advisor and met them in secret, but by the point she met the flying baboons on the tower, she was ready to drop the act.
