Does Thousand Tailed Watcher affect Ruin Runner?

Yes — Ruin Runner gets -3 Might when Thousand-Tailed Watcher is played.

The Watcher's trigger doesn't "choose" or target units; it applies a global reduction to all enemy units, so Ruin Runner's "can't be chosen" protection doesn't apply (Rule 757). Its Might drops from 5 to 2 (minimum 1 clause). The effect snapshots the board at resolution, so units played as a reaction before it resolves are affected, but units played later that turn are not (RiftJudge FAQ #11360).