That depends. If you have somehow bypassed the anti-piracy measures on a porygon to download one illegally, you could face hefty fines or jail time (depending on your country and its interpretation of pokémon theft), never mind a lawsuit from Silph Co. itself if you attempted to distribute an illegally downloaded porygon. In short, with the government and Silph Co. itself, I would say a lot of trouble.
However, should it be of any comfort to you, when it comes to the storage system and its involvement with all of this, you would likely receive a high five and a job offer, given my partner’s recruitment history. —LH
So would this piracy have any effect on the Porygon itself?
This depends on the porygon. As with all pokémon involved with thefts, some porygon may experience stress, panic, and all the other psychological damage associated with being forcibly removed from its trainer or home. Other porygon see no difference between one home and another and may not mind as much. And still others actually prefer to be removed from its former trainer for one reason or another.
If this is more of a matter of whether or not illegally downloading a porygon would affect its code, fortunately no unless we’re talking about porygon-z. But to be fair, porygon-z is unstable as it is and has been known to suffer ill effects from entering sleep mode.
The Pokédex According to Bill 