It depends on where you are from, though the characters themselves also think different. We will never know.
In the game's Spanish version, Quina is referred to as "she", and it is same for Quale (renamed Quera), while Quan is "he". In the German version however, Quina is always referred to as "he". In the French version Quina is "she" whereas both Quale and Quan are "he". In the Italian version, Quina is said to be female, like Quale (renamed "Quera"), and has rearranged with Roman dialect.
Quina can equip female-only equipment like Lamia's Tiara, while s/he cannot equip the Pearl Rouge add-on.
If Quina is weakened, Zidane will not take damage in place of him/her with his "Protect Girls" ability like he does to Garnet, Freya, and Eiko.
Although the pronoun "s/he" is mostly attributed to Quina, only masculine possessive and demonstrative pronouns like "his" and "him" are used, while the feminine pronouns "her" and "hers" are not. Most languages use the masculine pronouns if the gender is unknown.