It still exists in Ingress.
[EDIT: Removed link to wrong post, darn it.]
OK, this link is better. While it talks about why a new wayspot may not show up in a particular game, the same thing will can happen for existing wayspots if the world around them changes.
Why hasn't my approved POI shown up in my game yet?
Basically, the wayspot is still in Wayfarer/Lightship. It sill shows up in Ingress. But, not in PoGo as you’ve noticed.