Hello
The BCD5 exam covers both EJB3.0 and JPA1.0
The v6 exams split
EJB and JPA into 2 exams covering EJB3.1 and JPA2.0 respectively
Now which version to do is up to you. Yet most people would suggest doing the latest version.
It depends on your comfort level based on the exam objectives and your experience in EJB and/or JPA.
I am in fact currently preparing for BCD5. I chose v5 exam because it covers both tech, able to kill 2 birds with 1 stone, company is still using
Java EE 5... well there can be a lot of reasons or excuses to do the earlier version.