The no explanation explanation
*spoilers*
I strongly got the feeling that the disappearance was carefully set up in such a way that it could never be adequately explained by any single cause, and that the debate could never be settled. For example, the red cloud and the geology hint at a natural disaster, but there's no evidence afterwards pointing to that (nobody finds any evidence of an avalanche, for example) and it doesn't explain Irma's amnesia nor the girls' unusual behaviour right before their disappearance, much less Irma's survival (lest anyone forget, this was in a hot, very dry climate - you can't survive long in such conditions without access to water, even if you're unhurt). An abduction might explain Irma's survival and even her amnesia (trauma), but otherwise there's no rhyme or reason to it - no ransom, no rape, no remains left behind and no reason why Irma would be left behind or released. Then there's the supernatural explanation (the supposed book's sequel goes down this route, but the authorship is disputed, at least on these boards, and in any case it would only be canon for the book, not the film), and the watches stopping sort of hints at this, but it's a bit outlandish in what is otherwise a realistic setting and doesn't really explain anything.
The advantage I see for the filmmakers (and perhaps the author too) is that it gave them complete freedom to manipulate events without having to make them plausible in terms of any one cause and to determine events entirely in terms of exploring what I feel the film is really about, which is everything surrounding the disappearance rather than disappearance itself: the end-of-an-era 1900 setting, the reaction of the school's community to this external shock, Victorian Britishness vs. a distinct Australian identity and, above all, exploring issues of conformity and social norms vs. asserting oneself as an individual.