Yes and no... if you are upgrading your BES using a cutover process, then you need to reactivate all your users IF AND ONLY IF you changed the IBM Lotus Domino server name.... A lot of people actually cutover to a new computer (may be in anticipation of more system resources usage for BES 4.1???) and that is when users stop getting email messages and they realized that they all needed to be re-activated.
The 4.1 Upgrade guide has a good chapter 6 describing this. Open up the PDF file and search for "reactivate" and you shall see the light
Cheers!