True, there are some dangers in the idea - piratical battleships, for instance, are a little crazy from a supply standpoint. That's part of why privateers die out with the Age of Sail. Ships become more expensive to maintain, pressing victims into service becomes harder... it'd be great to make post-sail piracy work in-game, but it's not really supported by the record, is it? Commerce raiders are the closest thing real-world, and the advent of the radio, the airplane, and the Geneva Convention all make those pretty easy to tie to their host nation. Case in point - nobody really thought the Graf Spee's victims were attacked by polar bears, icebergs, or a flock of winged monkeys; they were pretty easily identified as German. Even in WW1, on the cusp of the radio-airplane problem, the Lusitania's attacker was pretty clearly identified with a German U-boat, though the boat remained unidentified.
I still think that making the mechanism as universal as possible is the best way to go generally. The problem is that there are, as always, real issues that Civ4 doesn't handle. In the case of piracy, it's maintenance, crew strengths, and armament fabrication - cannonballs aren't that complicated, and powder is easy enough to come by, but the more advanced the vessel, the harder it becomes to maintain. In the modern era, I can see granting it to transports and submarines, but even then, there are some problems. Until the technological equivalent of the Napoleonic period, there's plenty of justification for it - the Vikings, Sextus Pompeius, the wako in Japan... problem is that if you promote a trireme, it could potentially become something much, much more advanced. There are also some problems with specific-unit exceptions. You can keep something frigate-sized crewed and equipped, but much larger for any length of time, and you really do need the full support of a nation behind you.
Incidentally - hadn't looked at it until now, but hooray for the new Darius. Looks much more... regal than the old one.