Since I only need discrete faceting I've changed method signature to public String getIndexingId() and now it's working. Thanks!

Great that this works for you.

Regarding your "feature request" - @IndexedEmbedded(includeEmbeddedObjectId = true, facetEmbeddedObjectId = true). This makes the object even more of a special case and as mentioned I think it is quite unusual to facet over the id. More important would be to be able to have multi value numeric field faceting. We look into it.