The nav file is likely embedded into the map file using [BSPZip][1] or [PakRat][2].

This isn't common for Valve's other games, as nav files can be [edited in game][3] and embedding it in the map prevents that.  However, workshop restrictions may mean we'll see more of this kind of embedding for CS:GO (and as of August 2015, TF2)

  [1]: https://developer.valvesoftware.com/wiki/Bspzip
  [2]: https://developer.valvesoftware.com/wiki/Pakrat
  [3]: https://developer.valvesoftware.com/wiki/Navigation_Meshes#Editing_the_navigation_mesh