I installed the "remove permalinks" plugin about a month ago and network activated it. This is also about the same tile I upgraded to WP 3.5.1. I didn't notice it missing until I needed it but today I went to change my privacy settings on one site and I've noticed that it is also hidden or gone. Could the "remove permalinks" plugin have disabled privacy settings as well or has the privacy settings been moved in 3.5.1? I disabled the "remove permalinks" plugin but seemed to have no effect. The permalinks options did not come back.