Yes, both BIS and BES works fine with 4.0.

And IE does not interrupt BES connection on my HTC S621. With 4.0, there is Internet Browser and Blackberry Browser installed (provided you have a BES account). So you can now use MDS. On the background, it installs two proxy addresses and when you run the Internet Browser or Blackberry Browsers, it runs IE with appropriate proxy settings.

Also, apps like Newsbreak was working fine, I didnt have to define a different APN, it was going via blackberry.net. For Windows Live and ActiveSync, I had to define the carrier's APN (internet.com, my carrier is Rogers). But even when I was using Windows Live, Blackberry messages were coming in fine. I believe with new radio on the new devices, it is able to connect to both APNs and manage data. But even with older devices, many apps would be able to connect to the net via one of those proxy fine.