IBM is releasing all its new products/updates to old verion under rational banner.Now coming to your question,
v5 of developer exam is for people working on websphere v5 app server with WSAD
IDE.
v6 of developer exam is for people working on websphere v6 app server with RAD IDE.
So its better to go for v6 exam as they will be removing v5 exams sooner rather than later.Also RAD/WSAD are built on top of eclipse rcp.So if you have worked on eclise,the RAD/WSAD will be superset of eclipse
All The Best