If the target creature is an illegal target by the time Unlicensed Disintegration tries to resolve, the spell won't resolve. It won't deal damage to any player. If the target is legal but not destroyed (most likely because it has indestructible), its controller is dealt 3 damage.
Whether or not you control an artifact is checked only after the creature is destroyed while Unlicensed Disintegration is resolving. For example, if you destroy a Fairgrounds Warden that exiled your artifact creature, Unlicensed Disintegration deals 3 damage to Fairgrounds Warden's controller.