Leonard Cohen asked what did Suzanne learn too early. Might be relevant, cause the song goes "Too young to know too much too soon bad wisdom" in almost one breath.
"I learned about the way people can treat each other and the way people, in extreme circumstances, will do things that they wouldn't do if they were thinking about it; how people, at a very basic level, will fight to survive and act in ways that humans would prefer to not think of themselves acting like. Those are things I think I learned pretty early. That was my sense of the world, as a place where... the world I grew up in was a very extreme place, it seemed to me. Maybe it was just because of my temperament. I don't think so. I don't think it was because of my temperament. I think it was the circumstances. Those were the first things I think I learned. I mean, I learned other things as well, but those were the things I learned too early. The other things I learned were things that children know, which are things of the imagination and things, you know, more spirit-like things. Things like, myth-like things. Those are things I also knew as a child."
The Suzanne Vega - Leonard Cohen Interview, October 1992 (http://www.vega.net/cohnint1.htm), transcribed by Eric Szczerbinski

"The bad wisdom is knowing something before you're ready for it. It's knowing something before it's time. Before. It could be sexual knowledge. Some kids take LSD too early. Bad wisdom is when you have too much too soon. You go beyond what you're prepared to handle (Spikey: compare with what Suz said to Fatima, a 12 year old boy kissed Suzanne when she was only 8, Suz was very vague about the whole story. She decided back then that she was too young for it. She also described how she became more serious after that particular day"
[...]
"Well the girl in the song, who is a girl with a secret, feels like the woman who walks in the street. And in that way she is in someway paying for her life with her body."
[...]
"In some ways, everybody has their own form of it."
Interview with Fátima Castro Silva in "Urgent Whispers" (http://watermarks.vega.net/urgent_whispers/index.htm)

"It could be, though you'd be surprised how many people insist, to my face, that it's about AIDS. I'm like, "Okay, whatever." It's actually a song about fear. It's a song about looking a doctor in the face and... It could be about child abuse."
Interview in The Onion Av Club, November 21, 2001, Volume 37, Issue 42 (http://www.theonionavclub.com/avclub3742/avfeature_3742.html)

Answering to the remark that half of the songs on 99.9F° seemed to be about child abuse:
"Not half of them, but some of them are, definitely. Bad Wisdom, definitely. And maybe As A Child."
Interview in The Onion Av Club, November 21, 2001, Volume 37, Issue 42 (http://www.theonionavclub.com/avclub3742/avfeature_3742.html)

Suzanne wanted to have As a Child and Bad Wisdom contrasted. That's why they appear one after the other. She has put the album 99.9F° together in a way that there would be the most contrast and it just happened that those two fit back to back. They're different and that's why she wanted to put them together (http://watermarks.vega.net).

In the Passionate Eye is a poem called "Very Fine Laws" where Suzanne (or whatever role Suzanne takes in this poem) tells to somebody about how she doesn't believe in 'their' fine laws. She says basically, 'look out of the window' and you'll see that they don't work. Showing that person a victim and saying that he / she doesn't like to see it, suggesting sarcastically to cover it up with a pillow. Next, she pictures the law as some sort of a floor or some sort of a hand, and that all people will eventually fall through the cracks or slippery fingers. She suggests "you may as well join us down here laughing". If we may believe what is said in "Bad Wisdom", the other person is her mother.

For the medical themes see the song 99.9F.

"The answer is actually neither. It's neither about AIDS nor about unexpected pregnancy. The problem I had in mind for that character when I was writing that song was the problem of incest. It's written from the point of view of a young girl who has experienced incest. I don't feel the need to put it in the song because, to me, it... I prefer to leave it out. [laughs] And to me, it just... once I'd left.. because originally, when I first wrote the song, I explained it in the first verse. And it just seemed like it was too much information for one song. And I...once I took out the first verse then I realized that it could be about almost any number of things, and I preferred it that way. But, the actual topic I was thinking of was incest, in fact."
Suzanne's Vega.Net Audio Q/A Session http://www.suzannevega.com/about/1996/audioqa2.htm

[it's about an] "unwanted sexual encounter at too young an age." A child at heart, The Montreal Mirror, January 28 to Febuary 4, 1993 Vega's muse won't let her forget, by Richard Bird