I searched the web for this question. I found some scholars answering that it depends on how Auto-tunes is used: if you are completely changing the voice to sound like music, it's haram, but if it's used just to improve the voice quality, it's acceptable. But I'm finding it hard to find a definitive Islamic judgment on this subject. Is there a fatwa?
I think this question is something like: Is knife Haram?
Having most of objects themselves is not Haram. Our usage of them can be Halal or Haram. If we want knife to eat fruits or kitchen work it's Halal, if we desire to injure some innocent it's Haram.
Auto-tuner can be used to play Quran, Halal music or Haram music. Having it is not Haram, but the application can be Halal or Haram.
And I said most of the objects, because some objects are made only for Haram use, like alcohol drinks or addictive drugs. Some scholars say having, selling or buying these types of objects is Haram also.