BES 4.0 and 5.0 are night and day. If it weren't for the words BlackBerry and RIM pasted throughout the application you'd never know they were the same ... I'm being serious.
4.0 had a very MMC look
4.1 looked like a real application
5.0 is a web application
That said, 4.1 was my favorite so far. Maybe I'll eventually like 5.0.
There isn't anything you'll need to do from the Exchange perspective. Make sure that you get a good backup of your BES and BESMgmt database before the upgrade however (just in case)
To get your CALs: KB10952 - Determine the number of client access licenses installed on the BES - Port3101.org : Your BES Connection