I believe you put the parent-child relationship for easy access. A parent-child relationship is primarily implemented for the ease of transformation, so if a parent's transform changes, all children are affected by it.
Solution 1: You need not implement any parent-child relationship if you don't want the transformation hierarchy.
Solution 2: Godot has additional features like Groups for easier node access. So you can group all the enemies to an "enemy" group and you can call a method on all the enemies at once by
Solution 3: If you want to keep your parent-child relationship for any other matter and also want to move items globally, all you need to put the parent in the world origin i.e., Vector2(0,0) for 2D and Vector3(0,0,0) for 3D, set scale to 1 and set rotation to 0. Then all your child transformations will become the same as global ones.
Solution 4: Then again, if you want the solution 3 and also can't keep the parent on origin, you can use global transformation functions like