Is there a way to hide or disable all the window icons? I didnt find anything useful when searching on the internet, so I figured someone here could help me out.

Its this type of icons:
http://static.flickr.com/48/127408689_b73d645600_o.gif

I guess it could be done using ressource hacker, but I dont know which files to edit.

I dont think this has much to do with litestep, but yes reshacker would be the only way I know of