Because for one Bill is a complete genius and has a super secure impenetrable PC storage system and he was commissioned to design the firewall for individual pokeballs and what not. Also, hacking in the pokemon world is a capitol crime and offenders are hunted down and destroyed by the Interegional Encapsulated Pokemon Protection Agency, or IREPPA. << totally real.
and in case you haven't noticed, the villains of the pokemon world aren't exactly smart, so hacking is out of the question