The nouns and verbs in WordNet are arranged into is-a hierarchies. There are nine noun hierarchies and several hundred verb hierarchies. By setting the root node option, the measures that use the hierarchy information will join all of the noun hierarchies together with a single node and all of the verb hierarchies together with another single node.
Using the unique root nodes changes the behavior of the measures slightly. The path-finding measures (path, lch, and wup), will now be able to find paths between synsets that would otherwise not have had paths between them.
The root node is on by default.