You choose how the counters will be distributed when the ability resolves.

In some unusual cases, Vastwood Hydra will have enough -1/-1 counters put on it to make its toughness 0 or less. If this happens, the ability will still distribute a number of +1/+1 counters equal to the number of +1/+1 counters on Vastwood Hydra before the -1/-1 counters were put on it. For example, if Vastwood Hydra has two +1/+1 counters on it and three -1/-1 counters are put on it, two +1/+1 counters will be distributed.

The ability that triggers when Vastwood Hydra dies doesn’t target any of the creatures. You can choose to put counters on a creature with protection from green, for example.