Although not strictly intentional, you quite often can find SFF books which are monogender (though usually not monosex).
Left Hand of Darkness uses he. Everyone is a hermaphrodite, though.
Actually, everyone was completely asexual and agendered most of the time, except when they went into Kemmer. Then they were (temporarily) one or the other, and individuals didn't always become the same sex every time either. Hermaphrodite has a different meaning biologically--referring to an animal that has both male and female gonads and genitalia that are fully functional, though it can be simultaneous or sequential.
In the LHoD, everyone was referred to as "he" by the narrator, who is also the protagonist (it was in first person). The protagonist was male and came from a gendered, and very likely patriarchal, culture. I always assumed the defaulting to "he" reflected the pov characters own narrative biases, though I don't recall now if other characters also used "he" as the default pronoun in dialog.
Leckie's narrator/protagonist used "she" as the default pronoun in her non gendered society. In Leckie's world, everyone used "she" as the default, gender-neutral pronoun, though characters were often described as having traits (such as beards or breasts) that we associate with a given sex. It was gender being attached to a given body type that wasn't conceptualized in that culture--as I read it, at least.
I'd chalk these up to the choice of gender pronoun reflecting the narrative viewpoint of the pov character.
In
Halfway Human, a SF novel with a caste of genderless (and completely sexless, as in having no gonads or genitalia) humans, they were referred to as "it" in the narrative and by the genderless character who narrated part of their own story, but that reflected the fact that they were a downtrodden and abused group on their home world and the individual who made it off world was regarded as very strange within a gendered society. It was meant to grate, I think, referring to a person as an "it." Heck, I hate referring to animals as "it," because it seems to erase them as feeling beings with personalities.
I think it's different, though, when there are characters who are of a third gender, either because that reflects the biology of a species or of a human culture that has an acknowledged and named third gender. Then I'd be inclined to come up with pronoun for the third gender (or if a real-world culture use the one used by that culture). If someone is agender, bigender, genderfluid, or an alternative gender in a largely bigender culture, though, "they" is the most common preference I've seen.
I've gotten used to it. The only time it's tripped me up in books is when there's a context where it's not clear if "they" is being used to refer to a single character or if it's being used to refer to a group.