Hmmm; agreed. Some of the obscenity taboos aren't quite so brain-dead, either, at second glance. Sure, "cunt" and "vagina" aren't at all the same word, but I wouldn't say that if my web developers co-workers used the word "vagina" constantly that would be just fine.
As we're living in a reality where, you know, rape and suchlike happens fairly frequently, if I were a woman in a mostly male workplace and the word vagina was constantly bandied about, is it wrong that I'd feel uncomfortable?
Or say I was a middle-school math teacher who wrote all of his word problems in the form "so, one vagina is moving at 12 miles per hour due east, and...".
Talk is a step towards action, and it does matter what people say, as we are led to imagine them carrying out related actions, and we often assume (rightly or wrongly) some level of intent behind speech.
Maybe that's part of the reason behind some of the taboo words? Not to discount, of course, the unreasonably deep cultural discomfort with sex... but just, you know, tread lightly if you want to accelerate taboo expiration.
And it doesn't so much explain "shit", but that's possibly related -- I don't really want a discussion of poo-poo during lunch, for example, and there are very logical reasons that it might spoil my appetite (I'd rather focus my imagination on this delicious steaming burrito, thank you very much).