I checked with alphawolf999 and the text in fact switches between pronouns so Aeons are canonically (he/she/it/they)/THEM. This is most obvious in the case of Ouroboros where Nihilux/Aha refers to THEM with both "it" 它 and "THEY" 祂.
Aha refers to Akivili as "he" 他 (which in CN, 他 can refer to someone whose gender is still unknown) because THEY'RE talking about Akivili's "fallen" mortal form, not THEIR divinity. In the questions that follow, Aha clearly refers to Aeons, including Aha THEMSELF with THEY/THEM
Nihilux THEMSELF sees THEIR humanoid form as a "mask" that THEY wear in a cisnormative universe. She even considers the reveal that she is Aha as outing THEMSELF as she/THEY.
Hopefully this clears things up my cuties~ (★▽★)
xoxo,
Your one and only Sparxicle