Just got back. After Muir Pass (Southbound) the smoke got really bad at times. Obscured views, could taste it in the water, and I found it a little hard to breath at times. That said, there was a pattern to it. It almost always was cleared out by the mornings, came in in the afternoon, and was at its worst by late afternoon. Worst in the valleys, better higher up.
If I got to a reported;y beautiful spot that I wanted to see, I would camp there and wait till morning so I could enjoy it. It often pushed me on to hike more hoping the next valley would be better. It was better after Forester Pass. The view from Whitney was obscured, but still magnificent.
From what I understood the fire is not contained. Route 180 is closed which effects some JMT bailout points. For the latest news, search the 'Rough Fire.' Here is what I found...
http://abc30.com/news/rough-fire-gro...tained/957826/
I feel the fire has effected the number of hikers. There were noticeably less in the smoky areas. I presume day hikers and locals with more options are just canceling their plans. Rangers stated that it would likely remain like this for the season. I believe there are recommendations that people with asthma or heart disease avoid the area.
Yes, saw several people hiking with bandannas covering their mouths.
All that said, I had a fantastic hike, learned to deal with the smoke, have no regrets. If you have your permit for the JMT, I would not cancel any plans (baring health conditions). The positives out way this negative, and you will still have a great time. I would not be surprised to hear there are improvements in September. Have a great hike!