Lol tbh I haven't thought that deep about it. Ineffa is a "Multifunctional Robot For Domestic Application" so make of that what you will. I'm ngl, even tho I really like Ineffa, I don't know a lot of lore about her because I've been kinda burnt out from genshin lately and haven't done her story quest.
Afaik tho, Aino is the one who gave Ineffa her current design, and Aino is a small girl, so there wouldn't really be a reason for her to give Ineffa those parts. You could headcanon something like "the traveler secretly gave Ineffa a sex upgrade" or something among those lines. Or, you could argue that Aino just wanted her to resemble a human as much as possible, from head to toe, and/ or wanted herself to feel like a human and not be "left out" by the fact that she doesn't have a vagina and anus, so she gave her those parts too, even tho neither Aino nor Ineffa won't really have any functional benefit from Ineffa having those parts.
Also Idk if it is explained why Ineffa doesn't express much emotions despite being a smart AI, but it could be just a hardware limitation, or basically she doesn't express emotions because she is a robot.