Upon using a Gun cleaning kit on both a firearm (M16) and a magazine (10rnd Mag C) it only played the "Weapon cleaning" animation if I placed the item on the floor, and had the cleaning kit in my hands
To be absolutely clear, it still allows you to complete the repair, but it will not play the animation for weapon cleaning, the character simply moves their hands around on the floor as per the "Default" crafting / repairing animation.
Note: I have been unable to check if the animation plays if I hold the gun cleaning kit and drag a mag / gun to the "Combine" section of the hand.