As far as visible cloaks go, those were added as a standard thing with the patch to version 1.68 (the second to last one).
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NWNCQ is an override that changes many tileset textures. The files for that go into the NWN/override folder.
Haks can add practically anything for a module.
Hak corruption, especially on such a large scale, may have come from a spotty connection while downloading. If your internet service has improved, I suggest downloading a couple of test haks for modules to see if they appear properly.