I think it would be unfortunate if we all reflexively attacked the messenger here. Yes, the article series is uncomfortable reading - that's a good thing. Either the zoo community has a good rebuttal, or bad practices will be exposed and hopefully improved upon. I have never claimed to be an elephant expert and have never really had an opinion on whether they should be kept in zoos. It is, to borrow from Donald Rumsfeld, a known unknown for me. Having said that, I have some... Let's call them "impressions" that I'll throw out there in the interests of encouraging debate.
1) It's pretty clear to me that the "biological budget bomb" is real. Certainly it's real in Auustralia at the very least. I've seen nothing that satisfyingly explains to me where Luk Chai, Pathi Harn and Ongard are going to go when they're too old to remain with their herd. It also needs to be acknowledged that the breeding strategy being used here in Australia seems to maximise the chances of having male calves - we're quite probably talking about housing not three males but five or six or even seven within 20-25 years. It might be that there's a plan - it's certainly possible that Dubbo, for instance, will have no elephants by the time the bomb goes off. But that hasn't been explained to my knowledge. It's also true that Melbourne and Taronga's exhibits are already out-dated and would be seen as unacceptably small for the size of their herds if they were in the US. I believe if the importation was happening today it could only have been possible if the exhibits were being built at Dubbo and Werribee instead.
2) I would be really interested to see a timeline of elephant births and deaths. My guess is that the "two deaths for every birth" ratio in the US has evened out in recent years, as AI advances were made at the same time as many US zoos modernised and expanded their facilities, thus hopefully reducing deaths caused by environmental factors. It might well be that it's too early for there to be a clear statistical signal of a turnaround, but if my suspicion is correct then you could reasonably argue that the Seattle Times is blowing the lid on what zoos actually solved a decade ago. Of course, that comes with other challenges like the afore-mentioned male surplus.
3) The article makes much out of the use of bullhooks and chains. And guess what? So it should. The one discipline in which zoos need to be unimpeachable is animal welfare. I'm not interested in prosecuting the past but I certainly find the concept of chaining elephants for 17 hours a day, or of using bullhooks for anything other than life and death situations (say, when a keeper is at risk of being crushed if the animal doesn't move) at odds with the passion that any zoo will claim it has for its animals. We wouldn't accept zoos hitting great apes or big cats or bears. Why would we accept it for elephants? The argument put forward by one zoo spokesperson in the article - that the bullhook "doesn't hurt" the animal is patently ridiculous. Either it works as a negative reinforcement, or it doesn't.
4) There are clear Malthusian consequences from a business strategy that depends on regularly breeding elephant calves to get people through the gates. Yes, cute mammal babies are the lifeblood of any zoo but it's much riskier with elephants than virtually any other species, due to their massive size, long natural lifespans and complex, expensive husbandry requirements. The article makes two contradictory claims - that there's a "biological budget bomb" ticking and that elephants are at risk of becoming "demographically extinct" in 50 years. If I'm right and mortality is coming down at the same time that fertility is increasing, it's not hard to see which is more likely to be correct. Have a look at what has happened to human populations in countries where nutrition, sanitation, health care and the outbreak of peace have collapsed mortality rates, whilst the birth rate hasn't dropped nearly as quickly in response. And then think about what this means for zoos if the same applies to elephants.
5) If the allegation is true that AZA members agreed to present a united claim that "zoo elephants are thriving" in the face of contrary evidence, we should all be quite angry. Zoos exist in that uneasy grey area between being for-profit enterprises, municipal bureaucracies and vehicles for science and public education. The last two of those three categories (I would argue all three) have a civic responsibility to be honest and accountable to the public. There can be no education when the public statements are known to be misleading by those that make them.