40k voters, that's really not very many. So it's hard to say whether Trump had a 30% chance of winning or 40% or whatever, but the election at most was a toss-up.
Many random events could have resulted in a different outcome.
"Oh but it was only a 70% prediction"
You can't 70% win an election. Silver's prediction was that Clinton would win, but he was not super confident about it. The prediction was wrong. He was right to not be super confident about it, but the prediction of who would win was still wrong.
538's own post-mortem's on the event highlight that Trump was a very unusual candidate running in a very unusual election and as such the model was missing a lot of important information. They learned from the experience and adjusted the model going forward. Anyone complaining about that event is really just highlighting that they don't understand how statistical modeling works and are upset about how the model misled them or others which isn't Nate or 538's fault and is entirely on the consumer of their reporting. It's not like they didn't try to educate their consumers in their reporting.
The prediction is for one single outcome at one point in time. The prediction can not be that Clinton 70% wins it, or wins it 70 out of every 100 times because there is no 100 2016 elections. Those things may apply to his mathematical models, but obviously the models are attempting to predict the real world. Try to weasel out of it as much as you like, but the prediction was that Clinton would win, and the prediction was wrong.
"Oh he was only giving the odds for his model, you don't understand it's your fault he mislead you" -- no. Every analyst and pundit has a model or a system, obviously nobody thinks any of them can see the future. Nate Silver was very explicitly predicting the outcome of the election. As you can see from all his commentary articles that came out along with the numbers.
And yes, 538's vaunted models and data science fell over when encountering situations that had not been seen or anticipated or built on before, obviously. We didn't need Einstein or even Nate Silver to tell us that. That's the problem isn't it. All this hamming up of "data science" and "mathematical models" is meaningless. Your data and math can be perfect and correct, but if they fail to provide an understanding of the world, then they are perfectly useless.