James,
The plan for nested resources is to add them via rack middleware once JSONQuery support is ready. This will allow middleware to map nested resource queries to normal queries on the resource with added ("where project = X") requirements.
As an aside, I would recommend not using a project_id attribute in your note resources. Rather, I would recommend using a project's URI and calling the property "project" or "project_uri." That will allow clients to navigate your tree without having to know how to assemble structures based on assumed directory nesting and ID structures.
-Jon