Christ, people are whiney about the pronouns...
Okay, quick primer, in japanese pronouns arent commonly used to refer to people, instead of saying "im going to her place" it would be more common to say "im going to insert name's place". Having the chapter say "Now they have a job" sounds better in English than having Nao refer to Kou by name in every sentence, because English speakers dont typically do that
Now, as far as why "they" is used instead of "her", its because A) English has a shortage of gender-neutral pronouns and B) flipping between a male honorific and female pronoun feels weird to most readers. The -kun honorific is generally used to refer young men or juniors, and the friend group using it to refer to Kou is done because Nao mistakenly assumed Kou was male on first meeting them. Since the reader knows Kou is female, the translator is left in an awkward position, do they use the canonically used though incorrect gendered honorific and mix it with the opposite gender pronoun, or do they keep the honorific and mix it with a gender-neutral pronoun to cause less confusion
Tl;Dr - Stop bitching you whiney cunts. Its a pronoun, if it sets you off that much go back to living under a rock. Using "they" or "them" is perfectly appropriate