The following code will remove a command that is just below a top level menu, e.g. File -> Open, however if you try and remove one level below that, an ASSERT is thrown.

How do I remove a menu item (control) that is 2 levels down, e.g. File -> Open -> Something?

OnInitCommandsPopup(CXTPCommandBar* pCommandBar)
{
   CXTPControl* pCommandSubItem = pCommandList->FindControl(xtpControlButton, ID_TOOLS_SUBITEM, TRUE, TRUE);
   if (pCommandSubItem)
   {
       pCommandList->Remove(pCommandSubItem);
   }
}