Longtime Deso boater here.
Bugs are usually the worst after peak flow, as the water recedes from the reeds and bars. That's 1-2nd week of June. The worst I ever saw was a July 4th launch in '03, at Sand Wash. Very bad mosquitos.
But even then, they lightened up as the water picked up past Jack Creek. No-see'ums pop up in occasional halos, but it's usually windy enough to keep them at a minimum.
September is a great time to go - no bugs, cooler days, less crowds, nice color in the box elders and cottonwoods.