I am running with BB2 and no problems here, even though I can't give you any differences between a OS3.9BB1 setup and a OS3.9BB2 setup, as I always install both Boingbags on my systems.
I think you should try it out anyway. Just make a backup of your current setup and if something goes wrong you can always restore the setup.
If you decide to go on with the installation of Boingbag2 and decide to install the new ROM update, there is a risk that the computer goes into a reboot loop. At least my old setup with a Blizzard 1260 and SCSI controller did that. It apparently didn't like some parts of the new ROM update, but don't know if it was because of my IDE controller, or it was a problem related to the Blizzard 1260 board. Adding SKIPROMMODULES "scsi.device" in the SetPatch line cured that :-)