When Dewey is attempting to convince Scrooge that there's a fourth triplet, this is a reference to an error made in the original Ducktales comics series. Often times when artists were drawing the three triplets, they drew them all at the same time and doing the same thing. However, sometimes when one of the triplets had to do something individually, the artist would still draw three other ducks in the scene, making it 4 brothers and not 3 and it often got printed this way.
The experience Donald has of traveling in a space bullet back to Earth with with bright geometric grids passing him by pays homage to the film 2001: A Space Odyssey (1968), of which had a similar space vessel to what Donald escapes the moon with.
Phooey Duck is a character from the original Ducktales comics. He was brought into existence by a supercharged lightning strike that hit the triplets. He got his name based on the first word he said when he materialized into existence. He had the same personality as the boys and did the same things, but he did not last long. He would then periodically "hiccup" into existence close to the boys but not stay more than a minute.
The episode's title is a reference to the previous episode titled Whatever Happened to Della Duck?! (2019). The difference here is about what's been happening with Donald after he got stuck on the Moon when his sister Della managed to get off.
As Donald moves his arms to put everyone to sleep, it pays homage to the Game & Watch game Game & Watch: Flagman (1980) with a similar camera angle.