Pokémon Nature/IV modifying?

[Sturm]

I have a question about the Nature and IV modifying you can do on Pokémon you own.

I know it is not really legit if you do this to a Pokémon, but could Nintendo, or other people find out you have done it or not?

Or does Modifying the Nature/IV on a Pokémon not really effect it in any other way.

I have the dream radar Thundurus and Tornadus and well let's just say they didn't come with good IV's or natures.

Thank you.