My solutions for the pirate hideouts up to now has been pretty much scorched earth. I generally have sent in a single ship and played hit and run until the pirate fleet was either sunk or fled, then demolished the towers with it. I tried automatic brute force hits before too, fleets of captured pirate cogs (not much other use for them for me).
But both are inelegant. All those beautiful pirate ships, wasted. So, just how have other players managed the hideouts? Is there a good way to capture most of the ships without losing too many of your own? What do you think is the best approach?