I went through a questioning phase with respect to zoos a while back. Captivity is bad, so why would I support it? Breeding programs are important, but they're not enough to justify subjugation of animals, especially if some species only exist to be bred in captivity. However, the conclusion that I arrived at is that zoos are primarily for education. I wouldn't know enough about penguins, pandas, capybaras, or koalas to care about threats to their survival and habitats without zoos. I know that captivity is bad, but the benefits to the species in terms of awareness outweigh the suboptimal living environment of a comparatively small number of animals.
Also zoos take in animals that are injured or otherwise unable to be rehabilitated to the wild, often as part of breeding programs, so it’s not like “we captured a wild X to breed it”.
If you look further at the article you'll find it's hardly an exception:
but executive director Dr Lesley Dickie estimates that somewhere between 3,000 and 5,000 animals are "management-euthanised" in European zoos in any given year.
It depends on the species. It’s one thing to neuter a giraffe but if you have a flock of peacocks or a colony of 40 bats you are probably not going to do surgery on all of them, it’s also very hard on some of the smaller animals. Making an effort to keep only females or males would be an option for some species but not all, as they won’t always show their full range of behaviour.
The article does point out a lot of it is small rodents, but also things like tadpoles or fish. It can be extremely difficult to control their breeding (or even identify their sex without cutting them open) yet detrimental to their welfare to allow them to be overstocked. The real solution here is probably not invasive birth control techniques (even restraining an animal to pill them can be very taxing), it is more effort to share surplus animals with other zoos, wildlife refuges, wild release etc with particular attention to those that are prone to being culled. But again, transport is a huge stressor for animals, so you have to consider that the potential benefit to them should be more than the risk of worse welfare.
I think video documentaries provide the same if not better benefits without having to imprison animals. You can even show directly how their habitats are endangered (see Our Planet documentary series).
Walking through a zoo, watching the animals interact with each other, and with guests, reading about habitats, and experiencing an animal you've never even heard of before is a magical experience. I just got back from taking my daughter to a zoo 3 hours away from our house because she'd heard about okapis and wanted to see one. A documentary got her interested in the animal but the zoo let her learn a lot more.
Here's the thing. An animals environment can be completely fucked. Their environment is not going to get better anytime soon, and they are in the verge of extinction. Is it better to let them go extinct or put them into captivity? This is not a hypothetical, California Condors faced this issue as an example.
This is actually discussed in the article, which states that the raising awareness effect of zoos is very very small compared to its entertainment effect on individuals.
On the contrary, most people don’t read the educational plaques at zoos, and according to polls of zoo-goers, most go to spend time with friends or family — to enjoy themselves and be entertained, not to learn about animals and their needs. One study found the level of environmental concern reported by attendees before they entered the zoo was similar to those who were polled at the exits.