We are here @ DisneyWorld right now and have used the skyliner alot. Lightning seems to close it down pretty regularly based on my observations. The last 3 evening when the pools all close for lightning the skyliner also closes. We have a skyliner room view so its been interesting to watch it close down. We had friends get stuck at Hollywood Studios the other evening and they had to take a bus back since the skyliner was closed the other evening due to Lightning.
On the plus side even on 100 degree days the skyliners are pretty nice to ride in with the breeze and wind from the vents. Not hot at all unless you really get stuck for an extended period of time.