Some biomes such as the Atlantic Forest suffer from a shortage of native species in zoos. In this way, the few animals that live in this region are placed in broader sectors, generally related to the Amazon and the Pantanal. The same goes for the Caatinga, the Cerrado, the Chaco and the Pampas.
The Andes and Patagonia have very similar biodiversities, so an area dedicated to one is also almost completely dedicated to the other.
In addition to these, I would like to mention the following South American regions: the Galápagos, the subtropical forests of Chile and the Malvinas.
Finally, we have areas such as the Karoo, the Central Asian steppe, the grasslands of Manchuria and Japan.
These are the regions that come to mind when I think of places that are underrepresented by zoos.
I would say that in Brazilian and European zoos at least, you could fill in a very nice and complete Mata Atlantica zone with a nice conservation purpose. If I remember well, Bristol zoo had an area dedicated to this region (Zona Brazil).
In general, and outside of primates which are limited by large rivers, most south-american mammals are very generalist and can be found in different density across various types of biomes (jaguar being a very good example of versatility).
Chaco would be a very interesting habitat to recreate with one large, endangered endemic mammal being the Chacoan peccary.
Valvidian forests of Chile have a totally different track of species with very few present in captivity (magellanic conures and pudu).
In Africa, some zoos have started to breed endangered species of reptiles from the Cape/Karoo area but none have to my jnowledge dedicated more than a vivarium. I'am also surprised (and dissapointed) that no North-american zoo have tried to build a zone dedicated to the Horn of Africa with so many endangered ungulates. With the loss of Derby eland and ref-fronted gazelles, it becomes less interesting to have a West-african savannah area.
In Asia, I am surprised that almost no zoo try to focus an Himalayan foothills with a sufficient array of birds as this is a huge endemism center for many families. Sichuan pavillon (that focus more on Yunnan) in Praha and Plzen aviaries are to my knowledge the only examples. Another under-represented ecosystem are flooded plains from southern and central China. With Pere David's deer, Chinese water deer and various cranes and endangered waaterbirds wintering there, that could be an interesting area to develop.
Finally, I am not aware of any zoo seem to dedicate a specific area to Annamites mountains in Indochina, another center of primate and herps diversity and of huge conservation priority.
Would you say it is lazyness or lack of knowledge from zoo management ?