Well Jack, I know some basics about doing something like this. The paxton supercharger or a turbo use a blow through carb since that is how it is set up. The supercharger is blowing/forcing air through the carb.
On a 6/71 roots blower, the carbs sit on top of the supercharger and the carbs have air pulled from underneath by the engine/supercharger. They (The aftermarket) have designed carbs for both applications.
You could use just plain ol'stock OOTB carbs, Holley or AFB's on top of the 6/71, but for best results, a carb designbed for this application will get a good bit more power.
Sucking in water isn't a big thing. How much the engine is ingesting is. I see where this is of concern for you. I would not worry about this. If there was any concern (Or care) to being caught in the rain, then a scoop that I could flip around would be my problem solver.
