However, I'm curious about the expanded universe. Do any expanded universe works feature the development of intelligent starships, or starships that develop their own intelligence? In particular, do any of them feature a Starfleet starship with advanced AI capable of independent action and thought? Especially, ships developed past the end of TV and Movie canon, or that develop their intelligence past that point in time.
Yes one recent example is SecondGen White-Blue a Sentry . Their species of living technology is encountered in the Titan's expedition into the beta quadrant. When Titan encounters the Sentry's civilization it is revealed that every modern Starfleet ship could become sentient. Titan does become alive as well.
There is also the living civilization/ships/galaxies of The Body Electric an organism so powerful it scares the Travelers but not ever brave Mr. Crusher. In the book titled the Body Electric there are AI's of various types one of which is a ship.