In case anyone else finds themselves wondering this: (I asked support and they were kind enough to confirm)
Yes. It is safe to skin your legendary in the wardrobe system. It will lose it’s visual effects, but retain all of its legendary functions – ability to change stats out of combat, remain account bound, and will always be top tier stats.
So you can doll up your legendaries in the latest Black Lion Skin, or whatever else suits your fancy without worry of it breaking, like they once did before the wardrobe was released. Happy news! =)
(for me anyway)