The Central Park Zoo participated in the Eurasian eagle owl Species Survival Plan (SSP) by the AZA. In almost every SSP, there is a need for both institutions that breed the animal, but also institutions to house individuals that the SSP does not want to breed. So yes, for some zoos to house singletons of a solitary species IS a good idea. The SSP's job is to ensure that the populations of a species remain genetically diverse in the long term, so genetically overrepresented animals oftentimes will not be given breeding recommendations, and some individuals may never be given a breeding recommendation. Someone needs to house these individuals.
The fact Central Park has bred penguins is neither here nor there. What goes into managing penguins, a species that lives in large colonies, is very different than what goes into managing a solitary owl species. For penguins, oftentimes almost every zoo with the species is given breeding recommendations, albeit not for every penguin at the zoo. Don't get me wrong, it's great the zoo has bred penguins, but the management strategies and what it takes to breed penguins is very different than what goes into managing and breeding owls.
WCS did not maintain three separate polar bear populations. Each of the zoos with polar bears would've participated in the polar bear SSP, and would've housed individuals that are part of the AZA Polar Bear population. These polar bear programs also were not "poorly planned"- Bronx Zoo had a number of polar bear births over the years! The polar bear SSP overall right now is struggling, which is (at least partly) why neither Central Park or Bronx currently have polar bears, although I'm sure if the US polar bear population gets back on its feet, one of the WCS zoos may at least consider bringing back polar bears.