4.1.6 BES will run. RIM supports mixed mode even in this scenario for sure. But you will only be able to manage the 4.1.6 BES via the BAS interface. The BBManager will not run against the upgraded DB. One benefit however is that you can move users back and forth from the 4.1.6 BES to the 5.0 BES which may be helpful if you need.
Having said that, Enterprise Transporter is a pretty good way to get users from the old to the new DB if you want to go that route. And we all like clean new things, right?