I realize that I am a bit of a grammar precisionist, but I find the idea of usurping They for a gender neutral term is ridiculously arrogant. They is a plural form, so, in this case, it sounds like the Royal We, which is rather presumptuous unless you are claiming to be a sovereign nation.
"They" as a singular pronoun has attested uses in English going back centuries, and is commonplace in modern British English usage for that purpose as well.
(Which is hardly surprising, since it's perfectly mutually understandable used in that way, and therefore is much more likely to catch on in widespread usage than an attempt to construct an entirely new pronoun for it - which has been tried as well, over the decades, but feel free to try again if you want)
But NPC's currently don't even use gender based pronouns.
Doing a quick check, they try to avoid using third-person pronouns
at all, gendered or otherwise, when interacting with players or each other. The only place third-person pronouns show up much is in Galnet.
(There are a few cases where this leads to a somewhat stilted sentence, but given the 1% cruise liners and other such things, it's not very noticeable there either)
CMDR is as neutral as it gets.
Quick grammar note here: CMDR is gender-neutral, but is a title, not a pronoun.
(It could be used as a pronoun and perhaps by the 34th century it will, but it'd look a bit odd translated literally to 21st century readers - you'd get sentences like "CMDR's the most notorious pirate in the system" or "CMDR wants to trade")