Even thought John couldn’t remember he felt or thought he should do something for his daughter and that was his way. I think back then a little bit the old John was trying to come out. Plus he loved Claire and had a bond with her.
I think with Shawn and Belle leaving it was Shawn trying to get back happy times and remembering when he and his parents were on that boat. He needed time with Belle and Claire alone without the influences of Phillip who was always there. At least that’s my opinion. Not to mention he was always impulsive and this was one of the most impulsive things he’s ever done. Like father like son.