Ships are universally known to be a very special kind of units: they disappear when the faction is reduced to the rebel status, you can't command them in a battle, you can't hire them as mercenaries or bribe them, you can't re-train, disband or ransome them or appoint their captains governors. I wonder if anything of these has been altered in mods? I mean it would be cool to take two cogs of your own, add a couple of hired baggalas, bribe a dozen of carracks and go buccaneering at will.