The biggest difference between the regular islands and the pirate ones is that ye can't get back from expeditions to yer home stations to replenish tools. Pirate locations have their own wells with shorter timers. Plus, ye can take as many Super-swords and Bangs as ye like.
Starting from Rank 8, ye get additional tools to clear islands in pirate expeditions: Deckhands and Cannonballs. Ye can buy these tools in the Market (look for the pirate tab) or right in yer Shipyard.
Plan yer strategy accordingly, as ye won't be able to sail back to yer home islands. Once ye leave an island, it drifts off into the ocean FOREVER. Ye'll never see it again.