Cards that play to set aside area still function outside of play because that is how they are written. There are others like gates of hell, fishing boat, and even potters field that also work like that and the concept has been around for a while.
Part of why shipwreck was printed was because cards like those (fortresses in general really) were difficult to deal with because there were few good answers.
Shipwreck says it can target a fortress or site in play or set aside area thus why it can target those in set aside area.