Zendesk support informed me that tracking search words from the KC app and build a report on it in Explore isn't possible today. 

This feature would be really helpful in a KCS organization. I can track search words from our Help Center in the Support dashboard but I can't distinguish the words coming from an end-user or an agent. And since we want the statistics on flag, create, link we want everyone to use the KC app. 

Here is what KCS says about tracking search words:

"Search early, search often. It is interesting to know how often and when we are searching the knowledge base. This is especially true early in the adoption of KCS as people are learning the KCS workflow.  Here again, observation by a coach of knowledge workers doing their work and how they are using the knowledge base is important.  A helpful complement to observation is having reports on search activity.  The timing of the first search compared to case open and the frequency of searches done while responding to the request can be helpful information to inform the coaching activity.  Searching is an activity, so don't put goals on it!  The reports should be used to help identify coaching opportunities about the knowledge worker's behavior. The conversation should be about the behaviors, not the search indicators"

https://library.serviceinnovation.org/KCS/KCS_v6/KCS_v6_Practices_Guide/030/040/020/060