TL;DR: Yeah, Futa = Herm, but gender identity isn't the same as sex so technically they can fit in both NB and Female.
Hermaphroditism comes in a plethora of forms in real life (see "intersex") and while it is not impossible for a hermaphrodite to fit the standards of futanari, it is uncommon.
Bits of information about hermaphroditism.
Additionally, since gender identity is not determined by what kind of genitals someone has in modern understanding, a person with a female gender identity might well have a penis. In other words, yes, some women do have penises. It is also entirely possible to make oneself a "futanari" by undergoing partial gender reassignment, for example. Like by having only top or only bottom surgery, depending on what arrangement you start off with. Given the number of gender identities in existence its not surprising at all that some may CHOOSE to identify as non-binary, intersex, or hermaphrodites.
More broadly, it is one of the many possible layers of being intersex to have non-standard primary and secondary sexual characteristics. If you want to look at it from that lens of intersexuality (which affects 1-2% of the world population), it's technically more common than having natural red hair, or having a twin.
Futanari as a term in general is more fantastical and not really helpful because it seldom has a clear definition most agree upon. Generally, they are women with a penis. But whether they have a scrotum, or a vulva, or both, or neither, is entirely up in the air and up to interpretation since "Futanari" just means "of two kinds", is synonymous with hermaphroditism in general, and could cover technically any individual that fits into the very broad intersex spectrum.
Arguably, it's just as logical to see futanari in the female section as it is to see pre-op trans women in there, or pre-op trans men in the male section.
As someone who prefers playing hermaphroditic characters with female features but male genitalia, my RTs are in the Non-Binary section because I personally felt that's where I belong and where I'm more likely to find partners, but frankly; with their increasing prevalence in the Female section, I've been thinking of just copy pasting them there myself if ever I want more hits. I really wish we had many many, many, more labels we could use for our RTs, especially for the purpose of sorting to find what you're interested in. Given the type of character I prefer to play and my preference for feminine partners for example; I have the most success when looking through "FxM or NB" and "FxAny" labeled RTs. But I still have to sift through a lot because it's not everyone's cup of tea, and not what everyone means by it when using that specific tag. "FxNB" tends to just land me in the "people looking for specifically trans partners" boat, and there's a lot of people who have the expectation that all "chicks with dicks" will be 7'2" amazonian uber doms with a bitch-breaker the size of their femur who think of women and men alike as cum dumpsters and go insane if they don't climax seven times a day. ...which sounds INCREDIBLY specific but trust me; I've met SO MANY RPers with this exact expectation its a specific category in my mind. Then there's femboys and butches that are just men and women adopting behaviors and aesthetic from the other group, which get conflated under the whole non-binary/intersex umbrella making everything even more bloody confusing... ...and that's just the world we live in now.