Thanks! To answer your questions:
a) and b) The database is loosely coupled with the query language implementation, so it could be possible to change the query semantics without breaking it. That said I have other priorities for now (some adaptation for Node Webkit, porting it to the browser).
c) NeDB queries return vanilla objects or array of objects , on which you can use all the underscore functions you want.
d) Depends what you want to do. If you want to write a REPL I think it shouldn't be too difficult, and it may be a good idea to do one. In the meantime, since the API is the same as MongoDB's, you can learn NeDB using MongoDB's REPL :)