Could you make a version to actually duplicate the respective files? One of the big disadvantages of aliases at the moment is that they currently don't work in CoverFlow.

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The problem when copying is, that I can't find whether or not an icon is already copied.

Solutions I can offer:
a) create the structure as is, but at the same moment create an additional structure containing copies.
b) Yo may use this script to create a copy of the structur containing a real copy of the files:
mkdir copy ; ( cd OSX-Icons ; tar cBpfh - . ) | ( cd copy ; tar xvBpf - )
start it in the folder where "OSX-Icons" (the result directory) resides. You'll get a directory "copy" containing the same structure

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