Will too much exercise permanently affect my lung health?

Probably not. I know of no one who has developed lung problems as a result of exercise. It's far more likely to have other kinds of injuries like stress fractures, back problems, knee problems etc. From exercising "too much.".
Yes, for the better. Probably affect it for the better. An efficient heart can reduce strain to lung vasculature and your body will overall benefit. Extreme exercise overstressing the heart and causing wall thickening is possible, but in general benefits > risks.