Naufragare means "to shipwreck" or "to be shipwrecked." It's a vivid and dramatic verb that isn't commonly found in everyday conversation or every song.
In the lyrics, Elisa sings, "Mentre lascio naufragare un ridicolo pensiero" (While I let a ridiculous thought shipwreck/sink). Here, it's used metaphorically to describe letting go of a thought, allowing it to be completely lost or destroyed, much like a ship at sea. This poetic usage makes it a memorable and intriguing word.
"Gli ostacoli del cuore" is about what it takes to let another person in.
Elisa sings about a spark of magic that turns up right in the middle of the heart's obstacles, the guardedness and hesitation that come with getting close to someone. She keeps her most private thoughts wrapped up and looked after, then finds them already out in the open, and admits that she is the one who handed them over.
The chorus carries the song: so many things you don't know about me, so many things you cannot know, so many things to bring along on the journey we take together. Ligabue answers her lines with his own, so the song reads as a conversation rather than a confession.
Near the end the same list comes back with one word changed. Some of those things are worth carrying, and some are better thrown away. Choosing between them is part of loving someone.