1) You can open the webassist/kcfinder/conf/config.php file and add files to the "hide" array that you don't want shown.
2) Please upload an image to a folder that causes this problem and I can look into it.
3) I tried opening the file manager a dozen times and never saw this problem. Maybe it was related to the zero byte image you have removed?
The missing icons appear to just be that you haven't uploaded the images/icons folder.