Hi,
Regarding the system main menu still showing up when you've disabled the ACLs for all its sub menus we actually did a fix for that 2 months ago and it will be in the next version of HikaShop:
www.hikashop.com/forum/install-update/90...tem-menu.html#320978
Now regarding the affiliates menu, since you have the orders listing menu still active and the Affiliate sales menu is just the orders listing menu with a filter dropdown preselected, it uses the same ACL and thus it's normal you see it.
If you don't use the affiliate system, the best is to disable the affiliate plugin via the Joomla plugins manager. That will remove the whole menu from there.
If you do use it, then either you'll be stuck with that menu, or you'll have to edit the file menu / default.php via the menu Display>Views and add some custom code to remove the affiliate menu from there.