Allow me to preface this by saying that I was not among those criticizing Quiet's design prior to release. I am of the standing that if a creator wants to design something some way, that's their prerogative and who am I to try to fit my world view on someone else? Oh also, before I get into this bear in mind that I do like the character.
That being said, I am of two minds on the justification for Quiet's look. On one side, I think the idea of a character who essentially uses photosynthesis to exist is fucking cool and fits right in with all the other crazy shit in the Metal Gear universe. And following that it does make some logical sense that a being who breathes through their skin would want to wear a minimum of clothing. And with that we get into my other feeling on the justification.
To me, and I could be completely wrong here, it feels like the justification came about from Quiet being almost naked and not the other way around. What I mean by this is they didn't start with the justification and then design the character around that, it seems like they started with the character design and then figured out how to justify the design.
I don't know, it's just a feeling I got from the scene when Quiet becomes usable as a buddy. I still like the character and her abilities are fucking awesome. She can also be pretty fucking broken.