Contact decks are not normally reshuffled. I don't believe the implication here is that the discard pile is shuffled into the main deck, but rather than each contact has a pile of Piracy cards sitting waiting in their discard, ready to be picked up when the game begins.
Yes, and in addition to that, having just looked at the job cards while you were sorting out the piracy jobs, you now need to shuffle the pile of non-piracy job cards, so no-one knows what order they are in.
It's just a way of making sure all of the piracy jobs are available right from the start. The non-piracy jobs will slowly become available as players deal with the contacts.