Yes, flooding is bad. But not always as catastrophic as it's made out to be.
Anyway, yes, in areas that are degraded by acid rain, snow melt is bad.
1. Typically, in summer, a good portion of water flows through the ground, where even in the most infertile freestoners, there is SOME buffering, and the pH of the water will be somewhat better than that of the rainfall itself. In winter, the ground is frozen, and a much higher % of the flow is direct runoff. Hence, more acidic. With thoroughly frozen ground, snow, and rain melting that snow, it can be near 100% runoff.
2. Acid deposits on the ground even outside of rain events. Just in the air. Typically it lands on the ground, then much of it slowly sinks into the ground, where it's buffered. With snow cover, it lays on the snow. Snow melt is thus more acidic than rain. The longer the snow cover lasts, the more acidic it becomes. The worst case scenario is snow cover to not melt, and last all winter, storing all the acid deposition from a whole season. Then all to release suddenly in one massive rainy warm spell.
This is not unusual. For streams that are bordering on too acidic (from acid rain, not AMD), they're actually not so most of the year. It's the snowmelt events that lead to the worst acid spikes and become the limiting factor. Acid, especially temporary spikes, kill eggs before it kills fish. And this is one reason why you get good year classes and bad year classes in these streams, which a few years down the road, translates to swings in the fishable population.