Considering what we know of them, neither Hydaelyn nor Zodiark are good or evil. They are in effect highly sophisticated machines created for specific purposes; those purposes both had good intentions, but led to some very bad things from certain perspectives. (Zodiark did save the planet, but then the Convocation decided to let him eat new life for the purpose of necromancy; Hydaelyn was created specifically to stop Zodiark, but ended up wrecking the whole planet.)

Zodiark himself is not evil, as he only responds to the wishes of his creators (supposedly). That said his creators, being deep down no different from the mortals they abhor (no matter how much they try to deny it), can use him for evil.