In other words, don't delete it: this is where your custom stuff gets stored.
The defaults folder is one of the things I have put in my 0ther stuff folder. So yes, I do use sufolders there. Works just fine.
My own sample collection goes into an added folder under User Places.
I store my own samples in folders with names similar to those used in the Live sounds browser. This means they show up there too. But as I am using the Sound browser less and less I may change that.
You will notice there's a presets folder. That gets automatically created every time I save a preset but I keep it empty.
The trax folder is where I keep a range of default track setups. For example there is an external synth group(external instrument midi plus audio), a track I usae for rewiring to reason, and a couple of bus tracks.
Utilities is for all the other stuff I regularly need: Spectrum, Voxengo Scan, a little midi monitor, sewing kit, scissors, sellotape and painkillers.