I’m going to go on record here as saying that I think this will turn out to be a false confession.
Unfortunately—because it would be a good thing if this terrible and tragic mystery of over three-decades duration were to be solved. But the phenomenon of false confessions rears its ugly head as a distinct possibility here:
(1) the confessor, Pedro Hernandez, has (according to his defense lawyer) a history of schizophrenia and bipolar disease, as well as hallucinations. Of course, that does not mean he couldn’t be the murderer, but it also fits the profile of a mentally ill false confessor.
(2) there is so little evidence in this case that the usual methods of determining the veracity of a confession—does the alleged perpetrator have facts in his/her possession that fit the crime but are not in the public domain?—will be more than ordinarily problematic to apply.
(3) Hernandez confessed to the Patz murder shortly after there was a lot of publicity about the crime in the papers.
The phenomenon of false confessions is a surprisingly common and poorly understood one. Most often, false confessions occur as a reaction to the pressures of police interrogation, but that was not the case for Hernandez, whose confession was spontaneous. Such confessions are usually prompted by any or all of the following: desire for fame, feelings of generalized guilt, confusion about reality vs. fantasy.
Most of us have trouble even imagining such a thing, but nevertheless it happens with great frequency, especially in high-profile crimes. For example, over 200 people falsely confessed to the Lindbergh kidnapping back in the 30s, an even more notorious case than that of Etan Patz. In the Lindbergh situation, at least the authorities had a lot more evidence to match to the confessions to try to eliminate the false ones. The Patz investigators have almost nothing to go on.
[NOTE: I wrote "murderer" in the post title because I am also convinced that Etan Patz was murdered, probably within a short time of his kidnapping. But I admit that there is a remote possibility that he is still alive.]