Does Holochain see itself as a database layer or a layer underneath? If it is considered a DB, will there eventually be common DB tools like aggregation, GEOquery, etc.?

Holochain is an engine for both distributed data storage and distributed integrity checking on that data. So yes, it is a form of database. Holochain’s data primitives are entities and links, so it is very compatible with the concept of a graph database. Concepts like RDF/SPARQL and GraphQL are easy to translate to Holochain.

But data is distributed across many machines, so Holochain is harder to use out-of-the-box if you want things like tables, arbitrary querying, and other things that relational databases provide. We expect that many patterns, such as Bucket Set, indexing DHTs, and things we haven’t even dreamed up yet, will give you the tools you need.