There is where you are wrong. Shadowguards are barely trained, they are ment to silently kill some1 then leave. You are also forgetting they wernt trained to fight force-users, only anyone with no ability to command it. Force-users in this era were uncommon, as you know, so they would not be used to hunt them. That was Vaders job. Magnaguards were made in the time that force-users were plentiful, and were programmed to fight and even kill some of them.