What is the best way to store the object relationships in lucene? I need to be able to read them back easily and fast. Currently they are not stored in the lucene index and reading them from DB is slow.

Why is it slow? Are you sure that your Hibernate mapping is optimized? Are you using a second level cache? What's about lazy loading. I would first investigate "why" you think Hibernate entity retrieval is slow for your usecase, before I embark on using things like projection. Projection might bring you performance, but you will be outside the session lifecycle, meaning you won't have managed entities.

--Hardy