The following examples demonstrate how to access and manipulate Navigation settings via CSOM

PortalNavigationSamples2.cs

namespace Publishing.Navigation.Client.Samples
{
    class PortalNavigation
    {
        /// <summary>
        /// Print Navigation settings 
        /// </summary>
        /// <param name="url"></param>
        /// <returns></returns>
         public static void PrintNavigationSettings(string url)
        {
            using (var clientContext = new ClientContext(url))
            {
                var navigation = new ClientPortalNavigation(clientContext.Web);
                Console.WriteLine("CurrentIncludePages: {0}", navigation.CurrentIncludePages);
                Console.WriteLine("GlobalIncludePages: {0}", navigation.GlobalIncludePages);
                Console.WriteLine("OrderingMethod: {0}", navigation.OrderingMethod);
                Console.WriteLine("AutomaticSortingMethod: {0}", navigation.AutomaticSortingMethod);
                Console.WriteLine("SortAscending: {0}", navigation.SortAscending);
                Console.WriteLine("GlobalIncludeSubSites: {0}", navigation.GlobalIncludeSubSites);
                Console.WriteLine("CurrentIncludeSubSites: {0}", navigation.CurrentIncludeSubSites);
            }
        }

         /// <summary>
        /// Update Navigation settings
        /// </summary>
        /// <param name="url"></param>
        public static void UpdateNavigationSettings(string url)
        {
            using (var clientContext = new ClientContext(url))
            {
                var navigation = new ClientPortalNavigation(clientContext.Web);
                navigation.CurrentIncludePages = true;
                navigation.GlobalIncludePages = false;
                navigation.SaveChanges();
            }
        }
    
    }
}