Whether Atsu is queer in Ghost of Yotei is not clear, at least from the time I have spent exploring Ezo and completing missions (roughly 40 hours). There might be a small nugget of information hidden within the dialogue chain of a quest/side quest that would provide clarity on the question (or not), but I have not been able to find such yet.
Unlike Ghost of Tsushima's focus on Jin Sakai's conflict against the Mongols and the samurai ethics, Ghost of Yotei instead focuses on Atsu's personal quest for vengeance against Saito and the Yotei Six who slaughtered her family. Her character growth and actions are defined by the Night of the Burning Tree.
Meanwhile, you can check out our Ghost of Yotei: Complete guide and walkthrough for your completionist run.
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Atsu's character growth in Ghost of Yotei revolves around nothing but the trauma of her past
Ghost of Yotei does not venture into discussing Atsu's sexuality (in as much as I have found), probably because the tale it tells is consumed by the revenge quest. Much like her goals, Atsu's growth as a character before and during most part of the game is largely stunted by what happened during the Night of the Burning Tree.

As I mentioned in my Ghost of Yotei review:
"It is as if nothing else happened after that night for her. Being unable to move on, grieve, or process it, she has turned to revenge as the sole objective of her life, beyond which she is unaware of anything else."
While Atsu does make connections with other characters (humans, horses, and a wolf), she repeatedly reiterates her inability to build something meaningful apart from the rage that burns within her. By the time of Ghost of Yotei's ending, she begins her journey of change, but it does not depict an overwhelming one.
Did I miss out on any dialogue strand that hints at Atsu's sexuality in Ghost of Yotei, or have you found a side quest that does so? Drop a comment below, and I would love to check it out.
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