In issue #11 of Suicide Squad (2016), as a part of DC Rebirth, Amanda Waller is shot and killed. Her death is confirmed in issue #12.

Does Amanda Waller ever die?

Amanda Waller (died January 27, 2016), also known as her codename Mockingbird and her nickname The Wall, was the corrupt director of A.R.G.U.S. and the leader of Task Force X. She was killed by Shadowspire during their attack on the organization.

Does Amanda Waller know Batman's identity?

Waller met James Gordon at some point, developing a somewhat antagonistic relationship. She also became aware of the vigilante Batman and eventually learned his true identity, Bruce Wayne, from one of her agents.