How did the guys not notice Faris...

[Artemisia]

Faris was 5 when the pirates found her. Faris's age is given as 20 and she says to Lenna her last memory of her father was 15 years before. In flashbacks Faris is also seen being taught magic by her nanny and putting Lenna to bed and speaking to her with a child's vocabulary, so she definitely was not a baby.

Bartz and Galuf both had their suspicions about her (in the scene on the second floor of Tule's pub when they see her sleeping) and Galuf comments about her being too pretty to be a man when they discover she's female. There also appears to be at least one pirate who knows she's female and seems to be in love with her (again by conversing with pirates in Tule's pub)

So evidently it can be assumed she was found as a small girl and conditioned to believe she was a man for her own safety.

I knew from the beginning she was female, I found it to be poorly concealed. Maybe it was just the fan translated version I played, it wasn't very subtle!

[SCARY WIZARD]

There also appears to be at least one pirate who knows she's female and seems to be in love with her (again by conversing with pirates in Tule's pub)

That's present in the PSX and GBA versions, too, and oh lawdy does that make me laugh whenever I see it.
Aren't there historical accounts of female pirates parading around as males? I know there's supposed to have been one Irish woman who did it, as well as one or two more...

[Artemisia]

I'm sure there were many historical 'men' who may have not had the appropriate body parts
Being a women sucked back then, so it wouldn't surprise me if many masqueraded as men to get somewhere in life other than being a baby-making housewife.

[FarisScherwiz]

I noticed on the spot, when they said 'he' my immediate reaction was "ITS A GIRL"

Also if you go to the Pirate Cave in World 3 one of the pirates will remark that they found a child, he then remarks that the child was Faris and says that the child was a girl.