Ahh, the age old conundrum of D&D and ships.
It's such a knot of issues that all come together at the same time that makes ship to ship combat - something that SHOULD be pretty common in D&D - such a massive PITA.
Issues for Ship to Ship combat:
1. Scale. Never minding the 5 foot square scale, which really, really doesn't work for ships, and the 6 second rounds, which also don't work, there's the more basic issue that D&D really doesn't work for what I call platoon level combat. When you have 20-30 combatants to a side, D&D just doesn't work worth a damn. It's far too finely grained and there are far too many things to track for individuals. Which then results in all sorts of work arounds - grouping characters together for one - which again, doesn't really work when we're dealing with PC's.
2. The abstract nature of D&D combat. Again, here's something that is baked into the basic DNA of the game. How do you reconcile the fact that the combat system is not built on the idea of specific targeting but, then you need to use this system to specifically target and tell you what happens.

It's just not the right system. And you see it in the OP where he's targeting specific targets with a Mangonel. There's such a huge disparity between what the group is envisioning and what the system is telling you.
3. Time. This is a big one. Again, because of the scale of ship to ship combat, combats should be taking hours, or even minutes. Ships just don't move very much in six seconds. So, we start to fiddle about with what a round is. But, then it slams right up against the action economy rules in D&D. A wizard could very well blow most of his entire spell load in a single minute.
4. Spotlight - this is another big one. You've got one player piloting the ship. You've got another player shooting the "guns" (be they archers, or siege weapons or whatever) and three players sitting on their hands watching because there's not really anything for them to do. It's a pernicious problem.
Note, I have zero solutions to offer here. I really don't. Playing a naval campaign has been my white whale in gaming for a very, very long time. I've tried it in pretty much every edition starting in the 80's and it's never, ever worked well. It's one of the main reasons that I'm very reluctant to jump into Spelljammer despite absolutely salivating at the chance another naval based campaign and take another swing at the ball. But, there's this very loud voice in the back of my head telling me that I'm just going to be disappointed yet again. Go too deep into the simulation weeds and the players hate it because it's too dry and boring (unless you can get fantastically lucky and have a table of wargamers) or go totally abstract and you might as well just run a bog standard D&D campaign for all the impact being on a ship has.
I really, really want this to work and I've never found the right balance.