Most people who fantasize wiping-out mosquitos really only want to exterminate those species whose females drink blood. Most people to speak or write of wiping-out all mosquitos speak or write of wiping-out literally all mosquitos.
Mosquitos of any sort are pollinators (albeit not of food crops) and are prey of some predators (dragonflies, bats, birds). So flora and fauna would definitely be effected.
But, y'know, any change affects the eco-system. Only anti-humanists want the world to be as it would if humans were not here to affect it. Because the anti-humanist view is simply a religion, it has no felt need for a coherent explanation of why we should value such a situation; and we thus have no reason to accept that value.