You are absolutely right. However these are directories which then provide a link to the site. Therefore they end up actually having like lots of recip links with various, often poor ranked sites.

To me, this situation looks like a dramatic change in google. I've seen sites going banned over time but they are like here and there. This time it looks different. The entire section in my list, of directories which require a link back, has gone blank at once. This is too much to be a simple coincidence.