Are pieces in The Endless Dark still on the island?

Yes, they are still on the island for all purposes, even though they aren't in a land or on a board.

In particular:

Invaders in The Endless Dark block a Terror Level victory.
Presence in The Endless Dark prevents loss from Spirit elimination.
Beasts in The Endless Dark count towards preventing a loss against the Tsardom of Russia.
Towns in The Endless Dark count towards a loss against the Kingdom of France.
Presence in The Endless Dark can be destroyed by Events and Blight Cards that destroy Presence from each Spirit (but not those that destroy Presence from specific boards).

However, _showLink didnt receive the expected type {1}, and thus:

The Endless Dark does not count for loss conditions that are based on contents of a particular land, like Habsburg Mining Colony or the Kingdom of England.