We currently only generate API documentation for the daffodil-japi and daffodil-sapi subprojects. The rest of the subprojects and sort of considered a private/unstable API, and so it's reasonable to not include them on our website.
However, the daffodil-udf subproject is also a public/stable API, but it not currently generated and output to the website. Ideally this would all be merged into a single API that can be put on the website. SBT does not have a built-in way to merge API's from subprojects, but the sbt-unidoc plugin seems to be able to exactly that, and it even supports the genjavadoc plugin that we use for th Java API.
We should see if we can enable and configure this plugin to combine our API and UDF subprojects into a single scala/javadoc that can be put on the website. This could potentially be one method to easily define more public/stable API's by creating new subprojects and adding them to the list of things that sbt-unidoc merges.