I'd think it is because the name "Wikileaks" has higher visibility and meaning to the typical Australian voter than "Pirate Party". Despite common ground, they also have a different highest priority, Wikileaks being transparency, Pirate Party's being copyright reform. Separate parties will avoid tension due to different priorities.

Having two parties is not too big a deal in Australia's preferential voting system, as each party will probably pick up the other's preferences, meaning their votes will get transferred if they get knocked out of the contest.