Good catch. Actually, the scaffold doesn't support this feature currently, but as far as I know it could probably be done with a bit of help from a contributor Interested?
I'm actually surprised that anything shows up at all. Want to discuss more on email@example.com ?
Actually, I have the same issu. I have been deeply checking and indeed, there is no support for EMbedded ID (Talk about Many2many reationships and One2Many or One2one identifying relationships), for both persistence entities and endpoints too. (null id value exception).
Which kindda makes Forge useless for scaffolding from entities generated by Hibernate Tools.
However, I thing that embedded ids are implicitly supported when creating entities using JForge not Hibernate Tools plugin. Still investigating how to get a working example.