In the newest Vivre Card packs, extensive information regarding Yamato’s gender identity has been provided.
In her sex/gender section on the card, Yamato is referred to as “female” with no extra connotations. In the back of the card, she is more than once referred to with female third-person pronouns when described. And, in her description, she is referred to as “the Princess of the Beasts Pirates” and “the Oni Princess“.
The Vivre Card makes it very clear that it wants to address Yamato as female. Mentions of Yamato becoming Oden are made, but still done with female pronouns.
The fact is that in Eiichiro Oda’s work she identifies herself as a man, and those around her speak to her in that way. That is why it was thought that she was transgender, like O-Kiku (Kikunojo) who is a trans woman. But in reality, this is not the case with Yamato.
The Vivre Card clearly states that she is a cis female: that is, a cisgender woman. Is this information canon? It is, as Oda himself reviews and approves of this description.
In that sense, there is no discussion since it is an expression of the author’s will.
The choice of Hayami Saori as Yamato’s voice actress also confirms this revelation.