This bug applies only if you have two or more (EDIT: this might not be true, need more testing) stacks of throwing weapons. If you pick any weapon, be it one or two slots, even other throwing weapons, one of your stacks will be fully replenished.
EDIT: The ammo will only replenish if you fill up all four slots, that means that if you have a two-slot weapon and two stacks of throwing weapons you need to pick up a two-slot weapon to refill one stack.