The fact that there was a 4000 ton warship on the sea bed, which then vanished leaving only the indentation, suggests that somebody is capable of it. I've had a look round for species that might be responsible, and so far humans do seem to be the most likely candidate.

That's the easy answer. I'm thinking an alien ship resting deep in the pacific needed metal materials for repairs. Or a travel souvenir.

The De Ruyter sank in only 69 metres of water. That's plenty accessible with modern technology.