M5 Sandstorm missiles are not refilled when near Vehicle Ammo.
Edit: I just noticed that it would be a little bit stupid if the missiles were refilled immediately since they can be seen directly. A realistic solution would be to have - regardless of current amount of missiles loaded - an action menu choice like "Refill Missiles" if near a vehicle ammo box which disables shooting/driving for 1/2/3 minute(s) and refills the "magazine".