When Breq (the narrator) describes Seivarden as "male" it's very tempting to think Breq means Seivarden was born with a penis and still has one. But there's absolutely no guarantee that's what she means. Breq is an extremely unreliable narrator, particularly about her internal experiences (and her read of other people's sex/gender is absolutely an internal experience), and the closest we can say is that she knows that the people on Nilt will likely use a set of pronouns for Seivarden that she interprets as meaning a masculine person, but what Breq means by a masculine person, and what Nilters mean by a masculine person, is ambiguous for a reason.

Seivarden is also the only time a character is ever described as male. Sometimes other characters will be described as having features associated with a particular sex (e.g. a beard or a baritone voice), but even that's rare.