There is no final answer for your questions. However I can give you a few inputs on how to attack the problems.
Note, I am by no means an expert on nCloth, but I have used a few times to simulate cloth objects in our 3D images for Lego box covers.
I would start by modeling the objects with as few polygons as possible. I would try to stick to Quads as it seems that nCloth dynamics gives best results with quads.
I would start doing my simulations with low poly objects, just to see if it works as intended, to get the feel for the dynamics simulation and its cloth properties.
When I am satisfied, I would up the resolution of the object, or simply turn it into a subD surface.
regarding thickness, I would do the simulation on an object with no thickness, to avoid penetration in the surfaces. Then bake the simulation and add thickness simply by extruding the objects slightly. This is of course something that depends on the situation and experience. And you may also have to re-UV the resulting object.
The rest is simply to test, test, test.
I hope this helps a little. Good luck.
Senior 3D Artist,
Maya Software Manager & Maya Instructor
LEGO Systems A/S