When Thousand Tail Watcher is played, does Empowered Gangplank still get the -3 might or the +3 might?

Gangplank gets the -3 Might (6 → 3). He does not get +3.

His Empowered replacement only applies to "a spell or ability that chooses me" that would stun him, give him -Might, or return him to hand. Thousand-Tailed Watcher's "When you play me" ability doesn't choose or target anything — it programmatically hits every enemy unit on board at resolution (RiftJudge FAQ #7280). That's the same reasoning as FAQ #11758, where Blast Cone's non-choosing stun on empowered Gangplank still stunned him.

So the -3 applies normally and the replacement never gets an event to replace. Note that even for a choosing effect, the -Might event has to actually occur — a 1-Might Gangplank would snapshot to -0 and still get nothing (FAQ #11759).