Pretty much everyone who has poked fun at Deus Ex: Human Revolution has brought up the sunglasses, but it's usually stuff along the lines of "those are silly" and "how did they explain that to the insurance people".
This comic presents the question I've personally always had about them, which I can't remember seeing asked anywhere else. I can think of so many ways things could go horribly wrong with something like that.
That said, I also used to interpret Amanda's explanation in the first panel as correct, but when I went to double check the actual game canon, Jensen's eye augments are in his eyes, so... They are just sunglasses built into his face? I read that on a wiki, so maybe someone's just mistaken and there's more to them than just being retractable sunglasses? I hope so, in any case.
Whatever the shocking truth of Jensen's cool robot sunglasses is, this represents Grace's imagination / interpretation of what she's been shown, so it's fine. EVERYTHING IS FINE.