Magic Damage in Loop Hero is a stat that you can level up during an expedition which is basically a flat damage increase that is not affected by an enemy's Defense stat. This basically means Magic Damage functions almost exactly like standard Damage except it is particularly useful when you are faced with enemies that have a very high defense stat as it will bypass it regardless. Similar to other stats in Loop Hero you can acquire Magic Damage by picking up new equipment as you defeat enemies in the game.
The usefulness of Magic Damage is therefore situational and will be determined by the enemy you face. One enemy it is particularly effective against is the Skeletons that spawn from Cemeteries in Loop Hero. This tanky enemy is usually difficult to kill but with a high Magic Damage stat they can be dealt with easily and quickly. An exception you need to keep in mind is that Magic Damage does not bypass an Iron Golem's passive ability. You also need to remember that the damage dealt by Magic Damage will receive the benefits of the critical hit multiplier and it also impacts how much health is earned from Vampirism.
Check out our How to Get the Broken Geography Achievement
in Loop Hero which is unlocked when you place 10 cards you did not have in your deck.