It's strange but noticed that now with sitecore 9, there is no configs at path ~\App_Config\Include\
As per my understanding, now there is a config at path ~\App_config\Layer.config
which has following statements like:
<layer name="Modules" includeFolder="/App_Config/Modules/" />
<layer name="Custom" includeFolder="/App_Config/Include/" />
<layer name="Environment" includeFolder="/App_Config/Environment/" />
that mean from sitecore 9, layer structure introduced for modules, custom, environment and others.
Since currently after fresh instance with sitecore 9 there is no custom configs that's why
~\App_Config\Include\ has no configs, and if we wanted to add some of the custom configs then will come under the custom Layer.