Only a journalist who is worried about the possibility of being sued for defamation really needs to consider using alleged in reporting. The truth is an absolute defense to defamation. If you are confident in your reporting, and especially if you have good lawyers, then you don't need to hedge. (Source: was a lawyer who used to do some of this work at one time in my life)
Edit: If you are just reporting second-hand on someone else's work and haven't done the investigating yourself, then you might indeed want to say alleged whatevers.
"Presumed innocent" refers to the government not being supposed to punish an unconvicted defendant beyond what's practically necessary for safety (though reading up on pre-trial detention is... illuminating). It does not mean if we look at Jason Voorhees covered in blood that we all have to say "well, he's not yet gone to trial, so it's really only an allegation of murder."
Innocent until proven guilty is more of a criminal trials thing. Balance of probabilities applies for libel.
I'm not in the US, but suspect it is similar to the UK where reporters will use "alleged" if they're using the legal defence of "qualified privilege" - which allows them to repeat potentially libellous allegations without themselves being sued for libel. In the case of reporting on documents (especially those made public in legal filings) the documents themselves are subject to privilege, so the journalists don't need to use qualified privilege.
Thank you for explaining this in an easy to understand way, my understanding all this time up until now (I'm also in the UK) was that until allegations get proven in court, they are only allegations! I guess there are different standards for criminal and libel trials
Edit: If you are just reporting second-hand on someone else's work and haven't done the investigating yourself, then you might indeed want to say alleged whatevers.