When Nanite is disabled at the project level with r.Nanite.ProjectEnabled=0, clustered deferred shading stops working. This happens because the FDeferredShadingSceneRenderer::RenderLights method does not call AddClusteredDeferredShadingPass(), since this call is inside an if-block testing for ShouldUseClusteredDeferredShading, which returns false when Nanite is disabled. ShouldUseClusteredDeferredShading checks DoesPlatformSupportVirtualShadowMaps, which itself checks DoesPlatformSupportNanite which returns false if Nanite is disabled for the project.
DoesPlatformSupportNanite also uses bCheckForProjectSetting as and argument, which doesn't get used in the method's logic.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-367700 in the post.