If you do leave the negative ungrounded it does make it harder to troubleshoot, sometimes it's hard to find a reference point.
With the Negative grounded you always have a reference point in any grounded metal or building steel.
I think there is also an issue with instrument amplifiers becoming saturated for example if the wiring happens to be 100 Volts DC above ground (and how do you know it's not?)
I have seen systems where they had a pair of incandescent lamps in series with the center point grounded, this keeps the system referenced to ground and it does indicate if you have a ground fault but again it can have repercussions, they escape me at the moment.
Roy