I've lived in Parkhurst and Northcliff for many years and ride these areas 2-4 times a week on the road. Many of these times solo but there is always a risk which you can't avoid in JHB.
There was a mugging near Richmond the week before last but think that was opportunistic. Other than that i would just be vigilant on the road where it is nearby the spruit because when muggings spring up, it's usually around those areas for quick get aways. I'm not a mountain biker but i wouldn't cycle the spruit solo at all.
If you ride the roads in the E2E route, they're generally busy with cyclists.