Why does the SR-71 Blackbird sometimes have dents in the nose?
The SR-71 had a detachable nose (photo #2), and could change between three different nose cones depending on the mission. I haven't found a lot of information on the three, other than what this site and this site mentions:


Training nose with dead weights
Radar nose containing a Side Looking Radar. This is probably the bulge you saw on the photos. 
Photo nose containing the optical bar camera, taking very wide photos of the ground.