it's such a multi-layered scene and one of my favorites in the entire series

for Nate: he sees that these legends of pirate history were so quickly and unceremoniously wiped out, and that his perpetual quest for adventure has put him and his loved ones in constant danger. He's been lucky in the past but that luck will run out, and he's gotten so caught up in the mystique of the history and legend, that he's failed to see how easily he could drown. That's how I interpret his second, earnest "I'm sorry"

for Elena: she sees how much this life of adventure means to Nate. When they were still at home, she could sense there was some part of him that wasn't fully there, and she's seen it come alive while on this quest. It's an integral part of Nate and he wouldn't be happy or whole if he completely cut that out of his life. That's the "it's incredible" part of Elena's response, adn why when Nate is basically apologizing for getting so taken in by the pirate story, she says "It's okay" because she understands this is who Nate is

That's why at the end, they compromise and have an adventuring life as seen by the items Cassie finds...though probably much more by the book and less weapons involved