When uploading documents for indexing/parsing to QnA Maker, it seems that the documents are still stored in the tool. Is it stored within the tool itself? Is it stored in blob storage behind the scenes? Are these documents stored as clear text or are they encrypted?
As per the Service Configuration page, an Azure Cognitive Search resource is used to store the indexed version of your uploaded documents.
The Azure Cognitive Service itself uses Sever-side encryption at rest, from this page:
Microsoft-managed encryption-at-rest is built into the internal storage layer and is irrevocable. Optionally, you can supplement the default encryption with customer-managed encryption keys. Keys that you create and manage in Azure Key Vault are used to encrypt indexes and synonym maps in Azure Cognitive Search.
More information on how this works is available on the Security Overview page.