Can Elder Dragon ability target Ruin Runner?

No, Elder Dragon’s play ability cannot target Ruin Runner.

According to its text, Elder Dragon’s ability requires you to "choose up to one enemy unit at each location" to deal damage to them. As confirmed by RiftJudge FAQ #8581, because this ability requires you to choose (target) units, it is blocked by Ruin Runner's protection ability: "I can't be chosen by enemy spells and abilities."