Why doesn't the world end when Arceus uses Judgment?

Inspired by this thread

Arceus is the God pokemon that created the universe. Thus - it is supposed to be omnipotent and powerful beyond our imagination.

Then, wouldn't it mean that one simple attack of Judgment could end the world? Wouldn't it be rather dangerous to capture an Arceus and command it like you want...?

Arceus was never defined to be the "God" Pokémon... he was defined to be a "god" Pokémon and there has never been any indication of omnipotence. Lots of religions / mythologies worship non-omnipotent gods.
Also, even if he was omnipotent, he wouldn't automatically destroy the world by using Judgment, as that would be the opposite of omnipotence (i.e. he'd be launching an attack that he has absolutely no control over). And if he was omnipotent then it would be impossible for any trainer to control / command him in the first place.

If Arcues is omnipotent, can he create a stone that he cannot lift? If he cannot create it, he is clearly not omnipotent but if he can and he cannot lift it, he is not omnipotent.

That's not a paradox. A "rock that cannot be lifted" is unliftable, by its very defintion. Meaning that anyone being able to lift it would be a logical contradiction. Omnipotence (at least by its common definition) still does not allow someone to break the laws of logic -- that would not be "omnipotence", that would be "nonsense".