If the targeted creature card is an illegal target as Dead Reckoning resolves (because it’s no longer in your graveyard, perhaps), you can’t choose to put it on top of your library. No damage will be dealt.

You must choose two targets as you cast Dead Reckoning: a creature card in your graveyard and a creature on the battlefield. If you can’t, then you can’t cast the spell.

Dead Reckoning deals damage equal to the power the creature card had while it was in your graveyard. This could matter if that card is something like Lord of Extinction or Tarmogoyf whose power is determined by a characteristic-defining ability that checks the contents of your graveyard.

If the targeted creature is an illegal target as Dead Reckoning resolves (because it’s no longer on the battlefield, perhaps), you may still put the targeted creature card from your graveyard on top of your library. No damage will be dealt.