I thought the justification for Quiet being naked was pretty dang clever. It's not at all what I expected. I expected something personal, some trauma, which would have been bullshit. But it's quite a functional reason. Though there are a few issues:
1. Kojima said it would make us 'ashamed for our words and deeds' or whatever. How the hell is this true? Bear in mind I'm only on Mission 18 or something.
2. Ifshe breathes through her skin so she has no scope-wobble (a great idea)... Why the fuck is she wearing clothes in the Prologue?
3. IfThe End could also photosynthesise... Why the fuck was he wearing clothes, while Quiet isn't? I suppose the breathing thing. But surely this means she doesn't need to sunbathe with her bra off.
On the one hand she's really well written and I do personally like the justification of the nakedness. On the other hand the tit-shots are lame. At least none of the characters in-game objectify her (yet). Sure, they're scared and apprehensive of her, but nothing sexual (yet), which is refreshing.
It isn't clever, for some of the reasons you listed, but number 2 is explained.
It's a contrived reason, not an actual one. They came up with a way where her being mostly naked works, narratively, but you could do that with anything.
It doesn't explain her choice of clothing, either, just why she wears so little.
And she's part of a few scenes, perhaps scenes you haven't seen yet, that I'd best describe as deplorable. I don't usually see scenes in games that way, but Kojima managed something special.