In Game of Thrones naval battles, do land units on the ship count?
In the board game A Game of Thrones: the Board Game, land units do not board ships, and thus do not occupy the same location. Rather, ship units allow you to treat two coastal locations as adjacent for the purposes of using March orders on land units.

From the 2nd edition rulebook, page 23:


  Any two land areas are considered adjacent for the purposes of
  marching and retreating when they are connected by consecutive sea
  areas (or a single sea area) each containing one or more friendly Ship
  units. In other words, Ship units in consecutively adjacent sea areas
  form a direct “bridge” for Knights, Footmen, and Siege Engines to move
  directly from a coastal area to another coastal area in one move.


As a further note, when using the Support order: whilst ship units are able to provide support to adjacent land or sea locations, land units can never provide support to sea locations; as on page 18: 


  Ship units may support adjacent combat in a sea area or a land area.
  Footmen, Knights, or Siege Engine units, however, may never provide
  support to combat in a sea area.


However, it would be possible, for example, to use a ship with a Support order to transport land units into an enemy-controlled location, and then have that ship support the land units in the subsequent battle.