Story-wise, Nael was introduced (all the way back in 1.x) as a male character. This was not something specific to the localized versions.
As the Japanese language is not as tightly bound to gender pronouns as are EN, FR, and DE, there are far fewer instances of Nael being referred to as a male in the JP version. This does NOT mean, however, that such instances are non-existent. For example, on Nael van Darnus’s introductory page on the official FFXIV website, you can find the following:
彼が推し進める「メテオ計劃」なる作戦は、やがてエオルゼアに「第七霊災」を招くことに……
That first kanji character ”彼“ is “kare,” or the gender pronoun “he.”
For all intents and purposes, Nael is, and always will be, a male character. He was born male and died male. But then entered Eula, who was not ready to let the world know the truth, and concocted a plan to fool the entire world (including the Garleans themselves).