The collection was ageing. The majority of those animals that had passed away, were old animals. Sadly collections will go through these stages. If your collection has a lot of older animals, it stands the reason that you will have a stage of losses.
The issues with enclosures, was for a long time, they were planning to move the zoo to a new site. Therefore, enclosures were not worked on, as plans were a foot for a new facility. Sadly, objections by the council and a lot of issues, has meant this plan is currently not going ahead, and has now led to a revamp of a lot of enclosures within the zoo, and new species acquired. There was very few empty exhibits yesterday, so not sure what was empty when you last attended, but that has certainly now changed.