I imagine this is just the first step in balancing them. I have heard they plan to make them have diminishing returns the more you stack. So full warning for eveyone, don't expect for this to completely fix the "issue"
If they're not also introducing a new type of stacking penalty, then I hope you're wrong about this because the stacking penalties we have currently are not of a type that I want to see on any of the ship components. Additive multipliers are rather poor stacking penalties, and on top of that the game doesn't currently have any way to apply a penalty for N additional components rather than N components, at least as far as I know, so even the first component you have will be suffering from the stacking penalty.