Mussels are filter feeders, so a substantial population will make your pond water more clear during blooms. That can be a positive or a negative depending on your goals.
Mussels can be a vector during the life cycle of certain parasites. Do you ever observe any grubs on your fish?
I assume you are too cold for RES in your ponds. I can't remember, do you have any pumpkinseeds? I doubt they can wipe out your entire population of mussels, but it might not hurt to add pumpkinseeds, or manage your existing pumpkinseeds to get some large ones, to reduce your population of mussels. (As long as that does not interfere with your main goals for your ponds.)
