No, it's not going away or shutting down. They still have their output and work being made and it's business as usual. It's just no longer a separately operated team or unit. The CN Studios and WB Animation teams will be working on each other's slate now.
As for the CN Studios offices at Burbank's Third Street, their days are now numbered since it's all but inevitable they'll put all animation employees in the WB lot a few miles away.