I agree with SecretSlaveClass. Skulls and skeletons are often associated with occultism so JWs quickly associate them with demonism. Some JWs associate anything grotesque or scary-looking with demonism, regardless of whether or not the portrayal professes to be occult in nature. A sci-fi portrayal of a grotesque-looking creature would very easily be labelled as "demonic" by a brainwashed JW.
Aside from it's occult connotations, the skull is often used simply as an iconic symbol of death. Thus the skull and bones symbol of the pirates is meant to strike fear in the heart of their victims that they (the pirates) are fearsome, murderous thugs who are not to be trifled with as they will not think twice of killing you if you fail to comply with their wishes or if you dared to defy them.
The skull is also used as part of universal signs used to label products as being toxic or poisonous.
It's possible that humans evolved a deep-seated aversion to the sight of skulls as this afforded a survival advantage. Early pre-humans who avoided being around skulls also avoided the local environmental hazards that killed the persons who became the skulls.