Yamato doesn't get offended by being called female or by female pronouns being used on her. She doesn't what to be a guy, she wants to be THE guy, Kozuki Oden. Kiku is very clearly a trans woman, Yamato is a someone who wants to be someone else. I don't think she's trans and due to her circumstances, either pronouns should work
So yeah, One Piece fucking slaps recently. I was so disappointed by the ending and epilogue of Wano, but every chapter afterwards was incredible. Shit's starting to get real and seeing Vegapunk, the SSG, CP0, Teach in action and all these other things that we've been waiting for since years if not decades is amazing. Legit one of the most exciting times to be a OP fan
Do they even get referred to by male or female pronouns? I haven't read enough of the original Japanese to know, but in that language "he" and "she" are used exceedingly rarely, only in niche circumstances--
Usually in a lover's relationship (a boy calls his girlfriend "kanojo") or someone of higher status might refer to someone of lower status and also of intimate relationship with pronouns, like a parent referring to their own child, and other weird edge cases. Like if Kaido talked to Luffy about Yamato (which I think was exactly ZERO dialogue) Kaido might refer to Yamato as he/she, but other than that I can't think of any context in the Wano arch where Yamato's pronouns would be used. And even then, using he/she there is totally optional and using names/descriptors are as or even more common. Like Kaido might easily say "that child" instead of "him" or just "Yamato".
Now I'm certainly Luffy DEFINITELY uses 3rd person pronouns for Yamato because Luffy does for EVERYONE. The thing with 3rd person pronouns is that they tend to have the risk of coming off as rude/derrogatory in Japanese, which is why they're used in those niche circumstances where affection is already a given. But the pronoun Luffy uses for EVERYTHING is "Aitsu" which is both derrogatory and affectionate-- you either use it for people you love/feel affectionate towards, or people you flat out hate. Which for Luffy, those two categories is like the sum total of all humanity-- there's almost no one he establishes respectful personal distance with. This is kind of why we love him, and also his rude/brash personality. But "Aitsu", usually translated as "that guy" is a gender neutral pronoun-- used for both male and females and even things (and for Luffy literally everything in existence). Luffy also similarly uses "Koitsu" (this guy), which is the same thing but talking about someone/something immediately present.
As you'd guess from Japan's more conservative culture and the lack of gendered pronoun use in general, gendered pronouns is not something the authors are thinking about much either.
So when you read a translation of One Piece or any other manga, 99% of the she/her/his/him you see is the translator's guess required by English grammar but not present in the original text. Usually that's not an issue-- except for Yamato here and similar characters.
That said, I think Yamato's choice to go join the guys in the men's bath is testament to his gender. Only question up in the air is whether or not he takes offense at "she/her" (in English) which may be up in the air due to lack of that actually happening in Japanese.