Ok, I have tried a couple of experiments and get the same results.
I have tried making a hard file using SFS and then after formatting it, I use DirOpus 4 to copy all the contents of the AmiKit: dir to it. Then I rename it to AmiKit and quit. Then in WinUAE I select just the hard file and it does boot up, but some of the icons are missing. Like Ibrowse, Aweb and several others.
The same thing happens when I set up my 2nd HD and use HDToolBox to set up a small partition using SFS and I even tried FFS.
I figured by copying all the contents that everything on the desktop would still be there, but for some reason a few disappear. I can still get to them via the AmiStart menu. Just wondered why the icons would leave just cause I'm using either a hard file or a partition on a HD.