This is probably a minor cosmetic issue but will help with the overall asthetics and realism of the gameplay...
I've noticed that certain armor and rigs you select to put onto your character have a pistol hoslter. However I've noticed that it always remains empty despite having selected a pistol as a secondary weapon.
Perhaps similar to having the primary weapons scripted to rest on the back when not in use, pistols can be scripted to be inserted to the holster on the right leg?