And this is where I had done a metric crap-ton of historical reasearch. I hunted down stats on a bunch of sailing ships of all sizes. length, width, draft, # decks, # of sails.
I then deduced some simple patterns, based on the length of the ship to get the other stats. In the end, you could define a ship by its length, and get the other factors for free.
Where this had impact, is once you know how many decks, and the length/width, it becomes obvious how many guns, ballistae or catapults you can put on it. Every D&D ship I'd ever seen puts in maybe 7 weapons on a ship. Taking the idea of the 100 gun warship, that same thing can be done with ballistae instead. They may take more space, but you can still pack in more than 7 of them.
This was something I'd realized pretty early on as well. One of my first 'DM PC's' was the pirate commander of a high tech sailing vessel called the 'Sea Griffon' that featured a broadside of 6 ballista on each side. I thought I was soo cool. "Look at me, I can give my NPC's toys you aren't allowed to buy." Forgive me, I was 12.
However, there is a reason why you never saw that sort of thing in the real world, and its not lack of space for it aboard the ships. The real reason you never saw it develop in the real world was the relative ineffectiveness of mechanical seige engines against thick wooden hulled sailing vessels. In the era where ballista were occasionally mounted on ships, those vessels were rowed. To be rowed successfully required the designers to put a premium on weight, which meant the hulls had to be very very thin. So, a balista might make some sense as a secondary weapon against a galley. By the great age of sail, sailing technology had advanced to the point that you could have very thick wooden armor belts along the sides of warships. As a result, war ships were often immune or virtually immune to the _cannon fire_ of a vessel that carried smaller guns than it could carry. Heavy cannon balls shot at 1000 -1200 mph would literally just bounce off the 12"-24" thick layered oak planks. A mere ballista bolt, fired at 1/6th the speed, would simply not be capable of doing significant damage to a wooden sailing vessel and would have had a fraction of the range.
That's the reason that what limited naval warfare their was in the real middle ages was dominated by static boarding actions where the tactics were essentially the same as those on land. Fleets would crash together and they'd fight from ship to ship. No one invented seige ships carrying banks of ballistas not because they were stupid, but because it wouldn't have been worth the cost. And that's the reason why when you see sailing vessels show up in source books or adventures, its usually something more inspired by Master and Commander or Pirates of the Carribean than real medieval naval technology.
That being said, I think it would be a mistake to tell people what to play or what they can't play. There is no reason why for the purposes of a narrative you can't just assume that heavy mangonells work about as well at destroying ships as heavy cannon (with perhaps more limited range), and if players want to replace a cannon load out on a man-o-war or ship-of-the-line with mechanical engines and pretend that it all works, then that should be an option. It's not 'realistic', but it works if you want for whatever reasons a game without firearms but with the drama of age of sail warships.
Historically, the big difference in ship designs is size got bigger over time, enabling larger weapon load-outs, etc. So pre-Pirates of the caribean/master & commander ships just need to be set to smaller sizes and the rest should work itself out.
Part of this is that cannon casting technology was improving at the same time as sailing technology. Prior to being able to cast larger cannon, you didn't need a larger ship. You only needed a ship as large as could carry your largest cannons. That was principally determined by the beam of a ship, and so since the ratio of beam to length needed to stay roughly constant in order to have good sailing characteristics, as the cannon that ships carried got heavier the number of heaviest guns that the ship could carry increased with it. But in point of fact, some of the highest gun counts were by great ships in the early 17th century, when guns were seen primarily as anti-personnel weapons that detered or aided boarding actions. This is in no small part due to the fact that small guns were much easier to produce with the available technology than big guns.
However, it was pretty much clear to everyone from the defeat of the Spainish Armada on, that the future was in bigger ships carrying bigger guns, because it was with bigger ships with bigger guns that the English beat the Spainish so badly.
What, you thought the English had smaller ships? You fell for British propaganda. If you go back and look at the order of battle, the Brits actually had larger warships and more large warships, and they were of the more advanced design - fewer big guns rather than many small guns.
