Given her voice, even before she had a body, she definitely sounds femme, just as all the other old gods sounded masc. But like you said, does gender even make sense for her? There would be a stronger case with her having a body, one she says agreed to the sacrifice long ago, which could mean Xal’atath specifcally chose a female body. But since she’s of the void it’s as likely that Inanis was vulnerable and easily manipulated by Xal’atath into agreeing to sacrifice herself to Xal’atath. So it could’ve just as well been that the body she had the best opportunity to inhabit was female.
There’s way too little we know about old gods in relation to things such as gender, and Xal’atath herself to really know. We at least know that between the 4 old gods (not counting G’huun as he is Titan made), they don’t have a set “look,” of C’thun, Yogg-Saron, and N’Zoth, they’ve all been portrayed as giant, rotund, and being stuck in the ground, because they’re embedded in the world itself. However, besides those core features, they don’t look like they even would be related to each other. Then Y’shaarj, ironically the only Old God we don’t directly fight since he’s been dead for so long, is typically depicted in a more serpintine manner as far as body goes, still was embedded.
Although now that I’m thinking about it, Xal’atath I’m pretty sure does at one point refer to presumably the old gods as “brothers,” so maybe there is more credence to them having gender than we think.