That line in Layout.cshtml is showing the navigation zone, which is one of the widget zones.
In a standard Orchard setup a Menu Widget gets placed in that zone. You can check on the Widgets page in the admin. This doesn't directly show the menu widget though. This is done by another template.
In most cases the easiest way to find out which templates are being used is to use the Shape Tracing tool, which is part of the Orchard Designer Tools. There's an intro to Shape Tracing in the Orchard Documentation.
There are several layers of menu templates and it is a bit tricky to find these in the shape tracing tool.
The templates relevant to menus that you may need to include in your theme are:
- MenuItemLink.cshtml
- MenuItemLink-ContentMenuItem.cshtml
- MenuItem.cshtml
If you can't find them in the shape tracing tool, then do a file search in your solution and copy these files to your theme.