That's an excellent point. Yes, it could. We find that these zebra and quagga mussels are what we call “ecosystem engineers”. They change physical aspects of the habitat, chemical aspects of the habitat, and the biology of the systems. They have literally transformed the way the Great Lakes operate.
Initially, I thought that those effects would be limited primarily to the shallower basins, such as Lake St. Clair and western Lake Erie. But now what we're seeing is that systems such as Lake Huron and Lake Michigan have been completely transformed by quagga mussels as they spread to those systems.
One of the results of this is actually a positive one, in many cases. For example, if you own a cottage on a lake, your cottage value is partially determined by how clear the water is. The clearer the water, the higher the value of your cottage. Ironically, if you had zebra mussels there, they might clarify the water and the value initially might go up.
The reason the water is being cleared is that the animals are filtering both zooplankton and phytoplankton, and silt and clay. Using their gills, they either consume that stuff, or they spit it out and it sits on the bottom of the lake. The net result is that you remove a lot of particles that used to live up in the water. They are now being deposited on the bottom of the lake. If it's down there, then it's not available for the carp species, which are filtering the water as they swim through it.
So ironically, you're correct that it is possible that the effects of zebra and quagga mussels could make it more difficult for these fish to do well in the Great Lakes.