CKAN uses two PostgreSQL databases:
CKAN's catalogue database, this is the first database that you're asked to configure when installing CKAN. This stores all the data for CKAN's data catalogue, e.g. the metadata associated with datasets and resources (titles, tags, etc.), the user accounts, the groups and organizations, etc. etc.
CKAN's DataStore is an optional feature that enables a Data API and data previews for files uploaded to or linked to from CKAN. This is a second PostgresSQL database, data*store* is just the name the CKAN uses for this feature. (The DataStore in CKAN has nothing to do with the Google App Engine concept of data store that you linked to.)
CKAN also has a FileStore which, if enabled, is used to store files uploaded to CKAN. The FileStore isn't really a database, it's just a directory on disk that stores uploaded files.