We don't use these deprecated methods in Errai UI or Data Binding. My best guess is that you have a @Templated bean that requires proxying by the container. If this is the case, there will be a generated subclass of your @Templated bean in the BootstrapperImpl that overrides all public methods. Since a @Templated bean must extends Composite, it will override these deprecated methods as well.
There's no real risk here. If a future version of GWT removed these methods the container would no longer proxy them.