You'll sacrifice Departed Deckhand even if you counter the spell that targets it.
2018-07-13 • wotc
If the spell that targets Departed Deckhand has no other targets, it won't resolve (because it no longer has a legal target after Departed Deckhand is sacrificed).
2018-07-13 • wotc
Activating Departed Deckhand's last ability after a creature has become blocked by a non-Spirit creature won't cause that creature to become unblocked.