For starters, while artistically incredibly impressive, the ship is way too big to be a seaworthy mid-19th century ship (and apparently being a pirate ship, which would be anachronistic for the era as the Golden Age of Piracy ended in the 1730s and a ship of that size would be an easy target for navies). Just eyeballing it, her decks alone (to exclude the massive bow) seem to stretch up to 90 meters long and a beam (width) close to 30 m amidships. The deck length puts you in between the HMS Victoria, the world's largest wooden warship at a hull length of 79 m, and the schooner Wyoming which was the largest wooden ship of all time with a deck length of 107 meters and had constant structural issues. Even so, Victoria was the wider of the two and had a beam no wider than 18.3 m. Barring falling apart entirely, a ship of that width would have trouble cutting through the waves.

As far as services and utilities go, it really depends on the ship and what the mission is, and a civilian vessel can really just do whatever makes the most sense to the owners, same as a modern ship. I would start by just looking at various cutawayson the Internet for inspiration. Most large naval and commercial ships had cooks who operated at a galley (kitchen for you landlubbers), but because space was limited on a ship even the caboose wasn't often a permanent fixture. Everything on a ship can be squared away and converted into another purpose. Most of the crew didn't have a dedicated eating area; apart from the captain and main officers, warrant officers and enlisted sailors ate either at the gun deck with simple tables that could be put up and easily stowed, or in their cabins at the forecastle -- if the ship had them, that is, otherwise they'd also be sleeping in the gun deck with hammocks in between the cannons instead of tables.

Generally it was just a boatswain in charge of everything to do with physical maintenance, but the larger ships could have full on carpenters, sailmakers etc. But these would also be duties the rest of the crew would be doing or learning to some extent and so everyone had to work together. It wasn't too terribly uncommon either to have a blacksmith working a very small forge for making things like nails and basic tools, repairs, etc. Not too big, of course, don't want to be a danger to the ship or yourself. Speaking of which, an infirmary could also be expected on large warships, with the ship's surgeon's duties ranging from haircuts to amputations.

The rest of it all just depends on context. So if you're transporting animals, you're going to have specialists and equipment to care for the animals, allocate additional space if you're carrying passengers, etc. Just as long as it's not in the way and interfering with the ship's operation.

As far as facilities go, you're definitely going to need a capstan if you don't have one already. Gonna be tricky to lift an anchor without one. On the lowest deck before you hit the cargo hold, the orlop, that's where all your ropes, cables and tangly things are going to be stored. Since Minecraft has bell's now, you should definitely put a ship's bell on the quarterdeck and fo'c'sle. You can also definitely afford quite a few dinghies on that deck to serve as tenders or lifeboats in emergencies.

And since your ship is a fantasy ship anyway, I don't think you'll constrain yourself too terribly to this, just keep in mind the shipbuilding philosophy of everything having a purpose, convertible if necessary and out of the way if not.