I have no doubt this will be implemented. Even morrowind had it! If you ran around in your loin cloth, people would comment on your indecency.
I think as long as your clothing registered in one of the clothing slots, you were considered clothed - but NPC's would comment on whether you were well dressed or not based on your clothing modifier. Naked was essentially a clothing modifier of zero.
That said, a lot of BB clothing fit in slots that did not count as clothing, which is why you may have run into being accused of indecency, despite actually wearing something.
I do agree with the sentiment that your clothing should matter, though; and for more than an initial greeting. Well heeled merchants should treat you more roughly if you are dressed as a bum, and vice-versa. I also hold that some groups should immediately despise or mistrust you if you wear obviously necromantic or daedric clothing and armor - but that's just me.