The voter turnout was 23% in that election, which was boycotted by anti-statehood forces. I can't believe The Atlantic didn't emphasize that. It makes the article incredibly misleading.
As I recall, the reason for the boycott was there was some funny business about exactly what was being voted on. There are three options available, statehood, independence, and status quo. Any time there are more than two options in an election, it's impossible to be certain exactly which option is most popular. (Seriously. Look up "the election theorem") In this case, the "status quo" faction felt that the way the ballot was held would artificially inflate the support for statehood, so they boycotted.
I tend to agree with Joe Morgue that the US ought to demand the Puerto Ricans vote either in our out, and do away with this sort of intermediate status, but I feel that way about every US territory. Once you start trying to figure out what to do with the US Virgin Islands, the Northern Marianas, and Midway Atoll, it gets sticky, and it's understandable why politicians don't want to touch it with a 10 foot poll (pun, and misspelling, intended). So, although it would make sense to do away with the concept of "territory" for the US, I can understand why it won't happen.
Nevertheless, what is clear is that the people of Puerto Rico really are US citizens, and the response to Maria was shabby and indeed, shameful. Also, as I said some times early in the thread, there is one guy who could have done something to fix that, and he didn't. I don't blame the president for everything, but this time, it really was his fault.