Except keys are easier (at very least less tedious) to get, you need far less of them, and they don't require five click interactions constantly throughout the battle. You could easily eliminate many steps in the creation process and be done with it), and reduce the number of clicks required per use, and lose pretty much nothing.I would indeed consider pirating on par with other encounters, except for the loots. Tweaking the loots some(adding Granite types for example or maybe throw in a random ancient SOS) as others have suggested would be nice considering the hassle it is to make materials. Working the boat is a major part of the encounter.
Honestly I would have made "black powder" single rare ingredient craftables that being the small pieces of blackrock we already have as well as adding in larger chunks while mining, do away with the fuse, the ramrods, match cords, the swabs, all that junk. Blackrock -> Black Powder, Iron -> Cannon ball, Wood -> torch. The end. Balance it with different cannon balls having different damage and cool down counters, so you could fire a lot of light ammo or slower heavy. You could expand it from there but that's a nice simple system. Would have made boat combat FAR more accessible and fun for the majority of people, I would wager.