That does not answer the question "why?"
For those who deliberately or "unintentionally" lose their documents, it would appear that they do so AFTER entering Indonesia, otherwise, entry would not be permitted into that country in the first place. So, we should assume that nearly if not all of those joining boats from Indonesian ports had their documents up to or shortly before the time of departure.
So, they get rid of them. Why would they do that unless it was on the advice of the people smugglers. And, given the history of those miserable bastards, isn't it likely that it's just another one of the ploys used to assist the "asylum" claim, because I'm damned if I can see any valid reason for losing such important documents. Of course, there IS another reason - the person losing the passport has a criminal history or is a "person of interest" to our authorities and would never be allowed to enter Australian, one way or the other.....
Of course, IF they are being permitted to enter Indonesia without passports,etc, that raises serious questions about how serious the Indonesians are about controlling this trade.