They aren't really meant for finding cause and effect, but for capturing relationships. They're basically user centered ontology tools and act like a memory of things that you've learned about that are complexly connected. They also act also tools for inductive analysis and thinking -- keep adding data points and connections and you might start to be able to find a pattern.

Some of the best tools also let you construct timelines of various types to try to induce cause and effect as well. Analyst Notebook (a competitor to Maltego) has an excellent piano-roll like timeline tool.