Rookie Fisher, the depth refered to depends on what type of fishing. Motor mooching without a downrigger or jigging, would usually be the depth your lure/bait is located per your "depth sounder"
I'm a jigger and fish 90 to 120 feet. I am constantly re-familiarizing my jig to bottom. So when I say they are hitting at 95 feet, line angle is not a factor because I fish just a few reel winds off the bottom, regardless of the angle. If someone tells you that they are hitting at 45' in a known bottom area of 90', using a downrigger, they are probably giving you the numbers off their downrigger. If they are open about telling you, I'm sure they would articulate.