In holo backup, adb backup with system apps is said to be unsafe. I was and am not sure why it is. But I tried it anyway, and slept then when I woke up in the morning, my computer crashed. So I am wondering what is going on. (I tried other "safe" adb backup methods, and they did not crash my computer :) )
I doubt two things here: first, the crash of your computer is unlikely to be meant by that statement (I won't say it was completely unrelated, but at least rather a co-incidence). Second, the backup is unlikely to be unsafe – it's rather the restore to be concerned about.
Searching the web, you can find plenty of reports where a restore "broke the device", and left the user with crashing apps, not being able to read/write SMS, and things like that. Such happens especially when that backup was restored to a different ROM, or even just with some OTA in between. Structures might have changed, database layouts looking different (some columns dropped, others added), so "stuff" is no longer compatible with the backup. A restore would simply place the old files back, and thus might change parts of the system which now consist of more files/apps.
All those problems are rather unlikely to affect "self-contained user apps", but quite often happen with system apps. I hope this little excurse sheds some light.