WW seems to do that remix/recycle of music more often, and also more subtly, than other LoZ games huh? I mean the connections between the songs aren't obvious like the remixes in other games. The only one I've ever noticed was Outset Island having that one part that uses part of the Kokiri Forest theme. That's actually really cool since you can feel the nostalgia, but you really have to listen to hear the actual reference.
The Forest Haven theme uses something from OoT too I think, just can't remember right now ... the Dragon Roost dungeon theme mimics the Dodongo Cavern, and Jabun's theme mimics that of the Jabu-Jabu's Belly dungeon.
As for the pirate theme sounding like Kaepora's ... I do not hear the resemblance at all. Well, I can hear what you're hearing as a similarity, but as a musician I find no striking resemblances between the two pieces of music, besides the fact that they were both written by Koji Kondo and therefor sound like something he would write. There are very basic similarities in rhythm and structure, but I think any similarity you're hearing on this one is entirely coincidental, unlike the other intentional references in some of the other themes.
haha but that's just my ears. If it sounds like Kaepora's theme to you, then it should.