I second what PapaSmurf has said, we did 88 miles last summer in the SNP and I was able to hang in the vicinity of every shelter. We had the great VA Rain March, however, with a couple of days getting 3+ inches of rain while we walked. I can't remember which shelter it was, but I hung inside the shelter from the rafters due to the fact that the entire area around the shelter was flooded. The bugs weren't too bad, but we did have a few areas where the biting flies were so tormenting that we just had to move on rather than be eaten alive. They didn't seem to care about deet at all. I wound up pulling my buff down over my face in an effort to keep at least that part from being bitten. This was in mid-June, so I would think by the fall they should be gone, hopefully.
Hiking & Hanging is therapy, and much cheaper than medication in the long run. Carry on.