End Theories (Spoilers)
I think that Katie was abducted/killed and the director left many clues to show this point. The mother asks (something along these lines) "who would have wanted my daughter dead.... anyone" and the viewer is left with this same sentiment.
1) She texts Christian Slater's character that night saying "we need to meet". She could have told him she was pregnant, not taken Martin Sheen's advice and tried to convince him to leave his wife, then he could have killed her.
2) Martin Sheen's character locked the bookstore door and was super creepy when she went to talk to him. (esp. the whole "I will take care of your child" thing, which he denies when talking to the cops). He is a likely suspect esp because the viewer is only seeing him through Katie's eyes and not as he actually is (which the real version of him in the end is not as glamorized, mostly because he is a normal (not famous person) which is what I think the director was going for at the end of the film.
3) Her boyfriend or Justin Long could have been upset about the pregnancy and killed her.
4).Her mentally unstable friend, Joel, left her a mean voicemail and could have also been the killer,
I don't think she just randomly disappeared without a trace. The only part of the film that supports this type of end for Katie is the fact that all of her employers paid her in cash.