Fig
The Altruist
It's mostly speculation, but many fans believe that the rest of the pirates left Hyrule, been reincaranted (such as Link and Zelda), or was never mentioned again. Niko says that as his story the only remembers because if it wasn't for Link, the world would have continued to be under darkness. Though in Phantom Hourglass, Niko doesn't know about his adventure, even though Link was gone for only a measly 10 minutes.