As Japanese critics pretty much tore apart Tales from Earthsea, Hayao Miyazaki (after years of rifts and skeptical distrust of his son's handling of the movie) unexpectantly was present at its premiere and wrote to his son "it was made honestly. It was good." Goro cried. And it lead to Hayao pouring his heart out to create Ponyo as an apology to Goro.
The Morse Code scene is his direct message to his wife and Goro.
Hayao is apparently very good friends with Hideaki Anno, who holds him in high regards. As revealed in an October 2014 interview, Anno's mental health collapsed once more from the strain of directing Rebuild of Evangelion; Hayao told him that he has the option to quit if he wants but encouraged him to finish what he started, which turned out to be instrumental in Anno getting back onto his feet once more.