Removing empty nodes from zone.

- The zone is traversed, empty nodes are stored in the list of
  old nodes and their parents' children counts are decreased.
- This allows to remove parent-child chains.
- Removing of nodes is done in separate step because it modifies
  the structures used to iterate through the zone.
- Nodes are removed both from hash table and from the zone tree,
  but not deleted.

refs #1035 @20m