Actor Allusion: Morgan Primus, who is apparently "Number One" from the original Star Trek pilot (played by Majel Barrett). A Running Gag has her constantly compared to every character Majel Barrett played. And she eventually ends up inside the computer (Barrett also provided the computer voice in modern Trek).
Fridge Logic: Why bother giving Hermats their own set of pronouns? If the pronoun in Hermat language doesn't translate, they're welcome to borrow one from a language whose pronouns are not gendered. Chinese, for example has tā, which is gendered only when written, and then only when written in the logograms 他 or 她.
Pretty sure that hir/xie and already existed as potential genderless pronouns in English before the series was written.
In-Universe, the Hermats devised their own pronouns for use with other species, which may account for them not using previously existing ones. Also, Hermats emphatically do not regard themselves as genderless, but instead as having both genders. Burgoyne's reaction to Hermats being compared to the (literally) genderless J'Naii strongly implies that Hermats regard being considered genderless as an insult.
Holy Shit Quotient: Series average of 2 per book. That's not surprising when we consider some of the content: a giant energy being shaped like a flaming bird, which hatches out of a planet and later impregnates a starship; a one-eyed, one-horned, giant purple people eater; a woman who looks like Lwaxana Troi and Christine Chapel, and is immortal...who then dies, except that her consciousness is now inside a starship; a helmsman who regularly sleeps at his post and is part Greek god; a hermaphrodite chief engineer (hir whole species is hermaphroditic) who impregnates a Vulcan, of all people; and a book partially set inside a pocket universe that is, for all intents and purposes, a jellyfish. Basically, the series is one giant Mind Screw.