There are two ways:

  1. Select a query, wait for the query information window to open in the sidebar, and press the "Delete query" or "Delete query & data" button.
  2. Open the SupermetricsQueries sheet (go to the Add-ons menu, click Supermetrics and Manage queries), delete the rows with queries you want removed. After doing this, the queries will no longer return data when you run a refresh.