Ehh, I would argue against this based on his voice alone. It's true that van Hydrus doesn't have a feminine figure or boob plate armor, but no armors really have boob plates in this game (thankfully).
Anyway, back to the point: van Hydrus has a modestly deep, authoritative, masculine voice, and everyone refers to him as a man. His voice is clearly masculine, as are his voice actors; if van Hydrus were female, they might have given "him" a modulated woman's voice. Plus, the Legatuses seem to be somewhat based on their legion number's respective Final Fantasy antagonist; while we've only seen the VIIth's van Darnus emulate Sephiroth, the VIth's van Hydrus comes to prominence on the Floating Continent with the Warring Triad, suspiciously similar to Kefka. (Then again, Varis could go Kefka and van Hydrus could end up playing General Leo. Wouldn't that be cool?!)
In regards to the naming conventions, while the Garleans do have Latin-esque names, they aren't always straight-up Latin, and there's always the quirk of having a feminine name despite being male. There's also the possibility that van Hydrus is a transsexual, but I don't think this is the kind of game to touch on that (homosexual relationships do exist in-game, but we have yet to see evidence of transsexuals).
Now,
... but ask yourself: how plausible is it? How probable?
Personally, I don't consider it a likely possibility. There's too much evidence against it. (Then again I said the same thing about Nanamo being alive after 2.5.5, and look how that turned out.)




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