To supplement Wooble's great answer, here's what the docs say:
Datastore API Calls
The total number of times the app retrieved, created, updated or deleted an entity, or performed a query in the datastore.
Datastore Queries
The total number of times the app has performed a datastore query. Note that some query interface operations (IN and !=) perform multiple datastore queries; each individual query counts toward this quota.
So yeah, API calls include all retrievals, updates, deletions, creations, and queries, essentially anything calling the datastore. Only queries are counted for the other quota, which is why it's 1/3rd the size.