In the “old days” (4.x), I would have strongly advised against it. It seems that the feature has now settled in and is fairly stable. We were using it here when I started (on an R5 server on Win2000) without visible problems related to it other than long startup times after a crash. When we upgraded to Domino 6.5, it had a tremendously long conversion time that was not mentioned anywhere I could find – we were worried the server had locked up and were preparing our backout plan. We migrated away from it when we moved to iSeries, just one more “moving part” to have to worry about and the potential downside of any corruption wasn’t worth the trade now that we aren’t crunched for disk space.
What I think it really boils down to is how much you trust your backup solution and your hardware. You may want to specifically confirm with your backup vendor that the SCOS file is being backed up and can be restored in whole after a hardware failure and that mail files using it can be restored without taking everyone else on the server to a back-level SCOS. Sorry so windy.