(written from a Production point of view)
In the mythology of Star Trek, this city shares its name with the original name of the second Defiant-class USS Defiant. In reality, however, the city didn't (at least, not directly) provide the inspiration for calling the ship that prior to its renaming as the Defiant. (Star Trek: Deep Space Nine Companion, p. 693)
In an ultimately unused scene from the final draft script of ENT: "Stigma", Captain Jonathan Archer mentioned Sao Paulo, commenting that the extremely crowded planet Dekendi III reminded him of that location, or possibly Singapore.