Just keep in mind that Zequanox is not a chemical. It's a bunch of dead bacteria that, once consumed by the zebra mussel, affects the digestive gland causing its death.
http://cida.usgs.gov/glri/projects/invasive_species/zm_control.html
While they can't treat the whole Great Lakes, they can treat native shell beds, water intakes, marinas, and other sensitive areas selectively to try to mitigate some of the damage. Will be interesting to see what happens when some of these smaller lakes are treated completely.