With the ObjectName that NodeProbe uses, the JMX query can only match mbeans with type "ColumnFamilies". Secondary index CFs have a type of "IndexColumnFamilies", so the query won't match them.
The ObjectName documentation indicates that you can use wildcards, which would be the perfect solution if it actually worked. I'm not sure if it's some quoted vs non-quoted pattern issue, or if it's particular to the newMBeanProxy() method, but I could not get wildcards to match the secondary index CFs. Explicitly setting the "type" field to "IndexColumnFamilies" did work.