I’d go with number three. Sci/fi writers did not do nationalism very well, it was mainly human v alien or human v human in the sense of empire v empire sort of thing.
There may have been some authors who would have used a characters religion as a plot device or info dump in the past , but Its mainly a newer side of the genre.
In otherwords we were supposed to have been past religious friction.
Frank Herbert’s Dune universe envisioned a grand reunification into one true religion, but IIRC it just reunified Christian denominations (David Feintuch’s universe of space-opera crossed with Horatio Hornblower does the same thing). The Jews eventually popped up as a separate enclave in one of Herbert’s later Dune books, but I don’t recall anything much about Islam. Which is odd, given the desert motif and the frequent Arabic-sounding terminology.
Dan Simmons takes some nasty shots at Islam at the end of the second Hyperion novel, along the lines of the predominantly Islamic societies turning back the clock on civilization.
I’m positive I’ve read sci-fi with Muslim characters (one of whom experiences difficulties working out which way to pray towards Mecca in Zero-G thousands of light years from Earth), and several of the Religions in the Dune universe are clearly at least part Islamic, too.
The “No Mexicans in Science Fiction” thing isn’t true either- Bender from Futurama is from Tijuana, although he is a Robot.
The Fremen seemed to follow a variant of Islam (one of their grievances against the Harkonnen was “They deny us the hajj!” that is, they were forbidden to leave the planet to make the holy pilgrimage). Also, the Tleilaxu practice Sufism, though this is not revealed until Heretics of Dune.
Also, much of the Fremen-related terminology wasn’t just Arabic-sounding, it was actual Arabic.
I remember that Alan Dean Foster, in one of his (surprisingly very good) novelizations of the Star Trek: The Animated Series episodes, had a flashback to the construction of the USS Enterprise. The foreman of the orbital construction crew pauses in his work to pray towards Mecca as it rotates past, far below him. John Scalzi in the more recent Old Man’s War also refers to Moslem interstellar colonists praying likewise.