So while it's important to keep the Jackdaw upgraded, you can get away with using the same swords throughout most of the game. Most of the loot you'll find throughout the game comes via the Jackdaw and the ability to sail around and combat other ships. In many cases, it's faster and easier than sneaking around, especially if you're good with your swords. These missions can be completed by attacking every enemy in the open and making a huge commotion. While some missions require Edward to sneak around unseen, a vast majority do not.
Stealth has always been an important part to Assassin's Creed games, but Black Flag is a game about pirates.