Because Stumpsquall Hydra's ability doesn't target, you choose how to distribute X +1/+1 counters as its ability resolves. Players can't take actions between the time you decide this distribution and the time counters are put on the appropriate permanents.

You can't put +1/+1 counters on commanders that aren't on the battlefield.

You may put +1/+1 counters on commanders that aren't currently creatures (such as Tevesh Szat, Doom of Fools).

If Stumpsquall Hydra leaves the battlefield before its triggered ability resolves, you can still distribute the counters among any number of commanders, including none of them.