You can have topics that call other topics in Virtual Agent, so to accomplish this, I would use the first level as per normal, then when any of those top level topics are chosen, send them to a Topic with a Choice list (2nd level of hierarchy), and based on that choice, forward them to the desired topic.
Doing this, you should be able have as many levels of choices as you like, and it makes the topic design much cleaner, too.
