For now it's pretty flexible, we only enforce top-level dirs - client/, server/ and shared/ and then everything else is referenced through imports in .wasp file.
But I agree providing some best practices on the structure would be helpful - I personally prefer top-level grouping-by-feature (e.g. "billing/" and "reports/") over grouping-by-type (e.g. "controllers/", "components/"), but I know some folks prefer by-type, especially in the smaller projects.
We plan to add more starter projects and templates so that might be a good start. Is there anything specific you'd like to se enforced/suggested, based on how you like to structure your projects?