Parts with Magic Bonuses are called "Super Parts".
You can obtain Super Parts in two ways: by winning a Bet or by opening Boxes. The bonuses are completely random. They can add health or damage either to the part they are assigned to or to the different spare part (but not to the fused toolboxes). For example, you can have a Rocket Launcher with 20% bonus to attack, or the same Rocket Launcher that gives 10% Health to Classic chassis.
You can increase the Magic Bonus of the part by placing this part on a Bet and winning. Longer Bets give bigger bonuses. Please note, that you can only increase the Bonus up to 60%.
The parts with a 100% Bonus are called the Legendary Parts. They are very rare and can be found in the Supply Boxes. The higher the Box's tier, the more chance that it contains a Legendary Part.