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 and considers him his mentor. As revealed in an October 2014 interview, Hayao's guidance helped Anno through two of his life crises; the first was struggling with deep depression after completing Neon Genesis Evangelion in 1996, where Hayao told him that he understood him, since he had once been struggling with the same feelings, and advised him to take all the rest he needed to recover and wait for the urge to do something creative came naturally to him, ensuring him that his skills and talent would always gather people and money to any project with he would care to start on. When Anno's mental state again began to crack in 2012 under the strain of making 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.