This is really a problem of aesthetics, Nielsen's article is not relevant in the matter.
1) 3D icons are not 3D but fake 3D.
Most icons in a desktop are fake 3D nowadays. It starts to be a problem when 3D is not fake anymore, that can be confusing when interacting with it. (Little rambling : Apple's application dock is very close to real 3D because it can move a lot when your play with it but it does work when you learned the trick.)
2) You do not interact with the representation in the icon but with the icon as an object.
The fact that the illustration is 3D or 2D is not going to be as important as the treatment of the icon : location, size, shadows, with or without text etc.
You do not want your illustration to be confusing : let say your icon looks like folder, the user is going to expect a folder to open not an application. And to be coherent you want all your icones to follow the same pattern (aesthetics, size etc.). But at the end the illustration does not even have to make sense by itself. Most desktop icons are just logotypes.
3) It all depends on what you want to do with your icon
It is an icon for an action within an application ? to launch an application ? To illustrate a website ? To give some information ?
I would say: fake 3D, awesome flat design... It is all about aesthtics. It is like the size of ties, it comes and goes...
Focus on the interaction with the icon and avoid make stupid choices with the representation but be free to choose your own style. When you have choice.
But most of the time try to avoid the icon and turn to good old text.