Yeah, there will be Shenanigans. I am running this AP currently, and have some of the most creatively devious players it has ever been my pleasure to play with on the crew. Things I have learned:
1) Cleric = create water... the "need to get fresh water" thing DOESN'T WORK. Be prepared with an alternative reasoning for doing things.
2) Mage, Cleric, Druid, Sorcerer, Witch, etc = using magic (especially orisons like message, mending, etc.) to make "hard time" on the first voyage easier.
3) If your players don't figure it on their own, emphasize before starting the game that the players need at least one "face" character, and skills will be important, especially profession (sailor).
4) Unless you don't mind cutting your own throat against a good combat player in the second adventure module, change the weapon on Gortus Svard...
5) If you want to challenge players plundering the high seas, you need to use things like convoys, escorts, q-ships, etc. The base ships listed in book 2 will quickly be easily overwhelmed and boring.
6)In book 2, be sure to read the behavior patterns for the "beast of mancatcher cove" carefully... it makes a difference.
7)If your players are like mine, they will begin building a fleet long before the book says they will... read ahead.
8) Consider getting "Ultimate Campaign" for building (& charging the gold for) the inevitable pirate base.
I hope this helps.