Navigraph AIRAC updates are for add-ons to FS9, FSX and P3D and do not update these flightsims themselves.
So whilst the add-ons will show real life data, these flightsims may well be out of date for certain airports. This could include changed runways, ILS frequencies etc.
There are references in this forum and others to add-on scenery and AFCAD editing programs to change data in these databases. These are on a per-airport, manual basis.
You may also find suitable Flight Simulator navaids updates at http://www.aero.sors.fr/navaids3.html .
Please note this is FS9, FSX and P3D only.
Navigraph does provide comprehensive navdata updates for MSFS and MSFS addons at Navigraph Navdata Center