Shugenja compared to Bushi/Samurai are expected to be overpowered.
Unless you treat a shugenja as a thief class in a regular DND game.
Same as in DND, Wizards are often more powerful than Warriors in terms of raw damage or effects.
There is no way to balance this as if you look on the concept of a magic caster and a warrior, a caster is more often than not born with it, then it is trained, a caster can also become a warrior, but it isn't always true the other way around.
ie Ishikens
The allure of swinging swords and using bows isn't lost as some people like me do like playing samurai.
The hard part is incorporating elements in which even normal samurai have a job to do, instead of sitting in a corner while the shuggies fry up baddies.