I don't wear skirts to hike (except my ultra-feminine MYOG cuben rain skirt, of course), and I VERY rarely see other women on the trails in skirts, even though I live in a very warm climate.
That said, Anish (the current speed record holder for unsupported PCT thru-hike) wore thrift store dresses for most of her hike, so who am I to poo-poo that?
The JMT is one of the least brushy trails -- ever. But it's very often windy there, sunburn is a big factor, and most people do the JMT during bug season!
I did a section of the JMT last August, and wore shorts for most of my hiking. I prefer to be able to just flop down for a rest without worrying about flashing people (there's enough opportunity to flash when you're trying to wash yourself, LOL). Sunburn is a real concern, though, because so much of the trail is above 9,000ft, and long stretches are above tree line...which means the winds are pretty strong, too.
Long story short, I say "do it" if it's your fashion preference, but I'm not convinced that there are any real advantages to it (clothing weight, sunburn, modesty, elimination, etc.).