-San is just a formal/respectful way to address someone. Honorifics aren't gendered and are often associated with either status or relationship.
For example, friends might call each other -chan or -kun whereas you'd refer to your boss with -san. Ofc it changes depending on the person, but they aren't gendered lol
Btw, onii-san means older brother so idfk why he'd use fem pronouns for someone he'd refer to as "big brother." That would be onee-san if it was fem.
You can see in the title Nao is called "onii-san" on the cover he's also called a boy in the small text. That text is in english in the japanese version too. My assumption was that he would also be called onii-san in the raws, but seems like it's mostly "Nao-san".
Still I think it's a deliberate choice by the translator, considering the title makes the gender clear, and they also sprinkled in stuff like "salami" in the translation which i doubt was in the original.
The dick flashing was also on their credits with the title "itty bitty clit" or smth. Makes me think they're kinda projecting onto Nao
About the translations.
But for some reason the constant "Miss Nao" and even referring to him as a "she/her" kinda irked me lol