In order to get rid of icons (if you use x3):
1) in /usr/local/cpanel/base/frontend/x3/dynamicui/ create a new file called remove_items_dynamicui.conf
(the name of the file can actually be whatever as long as it includes dynamicui and is a .conf file, ex abc_dynamicui_xyz.conf)
2) enter one line for each item you do not want to show. For hiding mysql-remoteaccess, emailroute and legacy file manager, the following needs to be added:
file=>mysql-remoteaccess,skipobj=>1
file=>emailroute,skipobj=>1
file=>legacy_filemanager,skipobj=>1
You can find all file names to use for each icon in /usr/local/cpanel/base/frontend/x3/dynamicui.conf