BackupBuddy uses ‘activate_plugins’ capability to protect all its menu items. So when you revoke ‘activate_plugins’ from ‘Shop Manager’ role it will not see ‘BackupBuddy’ menu.

You may add ‘manage_options’ capability to ‘Shop Manager’ role. It will see ‘WitFTP’ menu then. But it will see ‘Settings’ and some other menu items protected by the same ‘manage_options’ capability. You may block them for ‘Shop Manager’ role using ‘Admin menu access’ module:

Block WordPress Admin Menu Items