1. No.
2. Evil PCs can do fine in this campaign. Having PCs that are divided against each other never works fine for any campaign. They probably all need to agree to live and let live or the game won't last with evil PCs. Given that, I wouldn't ban the spell, but I would make sure your players can handle this like adults who want to play a game together.
3. Have them plan out their gear. It will all get taken form them before the game begins, but earning it back is part of the game. I'd recommend telling them to bypass the standard suite of camping gear most people put on their starting PCs becaus they'll never need it. They'll be sailing their camp the whole AP.
Any other first time GMing advice would be great. I am planning on starting to prep for it now and get all the encounters and loot squared away to try and streamline the sessions.
A few thoughts:
1. Ditch the 'Rum Ration' rules aboard the Wormwood. Its an unnecessarily cumbersome addition that won't do anything to enhance your game. On the island, be ready to ditch the Botfly swarms as well if your PC's have no effective way to deal with them.
2. Think ahead of time how you are going to nurture the player's hatred for the Wormwood's officers while not provoking them to such a degree that they party wipe before its time for them to act. I also find it worked out better to have the PC's rebel before reaching Bonewrack Isle rather than after - being shorthanded and having the storm sweep them into the reef makes much more sense.
3. Encourage them to discuss ahead of time and come to a consensus as to how they are going to deal with captives when they capture a ship (this is more for books 2 and 3 but important) as well as how they feel about slavery. 'Evil' is fine for this campaign, but evil doesn't have to mean being horrific and brutal for the sake of being horrific and brutal.
4. The biggest change I made in book 1 was having Aron Ivy be alive rather than an undead. He was able to fill the PC's in on the ghouls on the island, the backstory concerning the Infernus, and even show them to the wreck (good chance to give them some extra loot). He also will be able to show them to the sea caves instead of relying on a chance peek through a spyglass ('those little sea devils caught and ate the last two of me mates - if they've taken one o' yore's, you can bet they drug em down to that thing what they call their mother'). In our campaign he was the ship's carpenter aboard the Infernus - which explains how he built his own stockade - and offered to fill the same role on the PC's ship in return for being rescued, including helping them with repairs.
This was my all-time favorite AP - if you have any specific questions feel free to pm me any time.
If you feel your players (or at least some of them) would enjoy playing an evil character, maybe consider building characters with each player seperately. Don't flat-out tell them they can play any alignment, but if they ask to play evil, allow it. That way the players playing non-evil characters are not going to be super-suspicious from the beginning. That will definitely reduce the number of characters with an ability to sense alignments. There will be some of those, but it will mostly be coincidence rather than planned.
Also, characters without an aura class ability don't have any alignment aura until they hit level 5. By that time, the party should have grown used to each other and trust each other enough that they don't care what alignment their teammates are.
And I don't think any of the ship's officers would tolerate big fights between crew members anyway, so that's another insurance until they have become a group that trusts each other.
I would say Evil isn't as much of a stumbling block in Skull & Shackles as Lawful is. This AP is probably most suited for Neutral and Chaotic PCs.
Evil PC's should give you no problem, just be careful to avoid any PVP, you need to keep the party together for the sake of the ship and crew (interparty fighting is a sure fire way to provoke a mutiny).
Be aware that there are a ton of NPC's to run and that will be with the PC's through out the adventure. The hardest part is the ships crew. I would make sure that the majority of the named crew and NPC's from book one that stick with them after the mutiny become officers (anything that has a seperate stat block). Any crew you get after that just make them faceless and nameless red jerseys and give them one stat block otherwise you may have to remember up to around 40 or more NPC's once they start getting crew from ports. I started giving each one a name and brief description (smiliar to the Wormwood crew in book 1)but gave up very quickly as it becmae impossible to remember who was who as new crew were recruited and old ones died off during ship battles or away teams.
Its also useful to level up the NPC's that are officers as the AP progresses, I tend to keep them 2 levels below the PC's. level the crew stat block up every now and again too maybe after 4 or 5 ship battles.
If you are not happy with the ship battles form the players guide then I suggest Fire as She Bears form Frog God Games. the combat system is a lot better but does need slight conversion work to fit (you wont need to look at this until book 2 though).
Some of the fights can be brutal and close to deadly, especially in the Wormwood Mutiny. Once my players gained control of their own ship, they had a NPC Besmara cleric aboard. I let that NPC level along with the players, and allowed them to purchase spellcasting from him (Sandara died off quickly in my campaign). The gave them access to raise, restoration and similar much needed spells, but since they had to pay for the casting, and since the NPC was allways at their level, and thus often charged more than the minimum needed for the spell, this easy acces came at a price.
I would run the game as stated in the book. Leadership isn't necessary for the crew.
I will try and keep the NPCs up to date. I no longer have a magus, and so I don't have any spell casters currently, but if I get someone who is, I will remember to keep someone to around so that they can get their spells.
I will be definitely be trying to keeping track of all the NPCs with. It'll be a fun task...
Should I allow leadership or will it be enough with the PCs collecting a crew for the ship?
I will take a look at the ship battle combat. I would like to get ahead of the players with the books.
There's never a time I would allow Leadership, but that's just me personally. I'd say it was especially unnecessary in Skull n Shackles unless you choose to let them name one of the many NPC's already presented as a 'cohort', though I've never really understood the difference (or the need for a difference).
In our game, Rosie Cuswell was the Second Mate through out the first three books until she eventually got a ship of her own and was replaced with a Tengu. Aron Ivey was a vital member of the ship's crew as a carpenter and all-around old salt until the fourth book when he lost his leg and retired to work on the PC's flagship. Sandara Quinn was a constant ally of the party, going on their adventures with them until her departure in book 5 and eventual return in book 6. Mardus Siggs and eventually Caulky Taroon headed the ship's 'junior' team. Any of them could be considered 'cohorts' I suppose but in our game they were just NPC's.