If a student disapparates in the first few weeks, I just assume he dropped the class. If this happens in the middle of the semester, I assume illness. What's odd is when a student goes missing at the end of the course. I've had them disappear with less than two weeks to go. Once I had a young woman (who was ace-ing the course) fail to show for the final exam, which was heavily weighted enough to sink her. She didn't skip the final or misread the exam date in the syllabus; she just vanished. Even odder is when students reappear. You walk into class, look up and there they are.
"I need to talk to you about what I have to do to catch up."
"Catch up? You've missed four weeks of class."
A retired colleague told me that she always played along and let reappearing students turn in late work, take the final, or attempt whatever they promise to do to make it right. They never follow through and end up failing anyway. Besides, she said, they might be crazy. The safe play is just to smile and make nice.
Most of the time you never find out why a student disappeared, but every so often you do. I had a guy this semester who showed up twice about two weeks into the term and then vanished. Saw in the paper he's now in jail.