Внесите следующие изменения
string dir = Server.MapPath(Request.ApplicationPath);
Для страниц ASPX, которые не находятся в папке администратора, используйте LINQ
string dir = Server.MapPath(Request.ApplicationPath);
// which will consider all directories (not excluding any)
string[] files = new DirectoryInfo(dir).GetFiles("*.aspx", SearchOption.AllDirectories).Select(o => o.Name).ToArray();
// To get files under folders except "Admin
// be careful about the case Word Admin - (ie. The Directory name has to be exactly same to avoid, otherwise convert both to lower case and compare)
var dirs = new DirectoryInfo(dir).GetDirectories().Where(q => q.Name != "Admin");
List<string> filesInDirs = new List<string>();
foreach (var dirName in dirs)
{
filesInDirs.AddRange(new DirectoryInfo(dirName.FullName).GetFiles("*.aspx", SearchOption.AllDirectories).Select(o => o.Name));
}