The dichotomy you present ("ask the question" vs. "report it as fact") is false. If you're phrasing it as a question, it's either because the answer is "No" or because you aren't capable of answering the question. Just tell me what you know instead of asking a question neither of us can answer.
The question headline is more compelling, but that's because it creates a false expectation that the question might be answered. It lends itself just as well to sensationalistic headlines like "Did Obama just give the order to nuke France?"
The dichotomy is not false, because the author of the article believes the reporter did find the identity. Probabilistically, he believes the likely answer to the question is "yes" (No, you cannot have a definite answer to that question. But this is true of any future question of fact or policy: "Will Obama win the election?" "Should we create a carbon tax?")
Given the content of the article, it would be an inaccurate title to say "reporter postulates that Michael Clear is the author of BitCoin" because the NPR article implicitly argues that Davis is probably correct. In this situation, the question is perfectly appropriate to express some level of doubt, but a likelihood of truth.
It doesn't matter — asking a question of the reader is still tacky and misleading. "Did a reporter just solve a BitCoin mystery?" either sounds clueless or promises far too much depending on whether you read the question as rhetorical. If you're the reporter, why are you asking me whether this guy "solved a BitCoin mystery"? (The answer is "To create the false expectation that the article will have an answer to the question.")
If the thrust of the piece is that you think Michael Clear is the author of BitCoin, then an accurate headline would be something like, "Joshua Davis just might have unmasked the author of BitCoin." This reflects the thesis much more closely than the original.
The question headline is more compelling, but that's because it creates a false expectation that the question might be answered. It lends itself just as well to sensationalistic headlines like "Did Obama just give the order to nuke France?"