I somewhat followed this case a long time ago, and only remember bits and pieces. But reading your guys' theory of a pregnancy seems likely. She could've gotten knocked up by someone who wasn't her bf, and she wanted to get an abortion so he wouldn't find out. Dad arranges it, but for some reason she doesn't reappear after like she is supposed to (after the abortion) so dad believes something happened to her. What if she couldn't go through with the abortion, and ended up going somewhere to have and raise the kid, not being able to come clean to her dad and friends and family about it so she stayed gone? Then, maybe years later she reconnected with her dad and begged him not to tell anyone, which would explain why he refuses to talk and wants media attention drawn away from her missing case.
I truly think he believed she was missing in the beginning, because he seemed so set on finding her and getting her story out. In the beginning. And he shut up when she finally came to him, years later.
Wow, I know that is a HUGE stretch, and possibly just seemed like a good story to me....call me, Lifetime!