Can Ruined Runner be targeted by Bone Skewer from hand?

Yes, Bone Skewer can choose a Ruin Runner from an opponent's hand.

According to the official RiftJudge FAQ #8682, Ruin Runner’s protection ability ("I can't be chosen by enemy spells and abilities") is only active while the unit is on the board. When the unit is in the opponent's hand, that protection ability is not active, making it a legal choice for Bone Skewer.