Does the world navaids installer for fsx and navdatapro/navigraph for fsx update vor/ils/runway frequencies/airways/waypoints the same way?

no .. neither the same way or the same data !!

 

there are three parts to this:

 

a) the world navaids installer is updating the fsx base navaid data including default airports (but europe only at this time)

b)the navigraph / navadatapro update is for your addon aircraft's fms

c) you need to use easynavs to update your airport addons.

 

they all align if you do the update at the same airac cycle !!