I believe all of the indoor shows are air-conditioned, including all the of the 3-D shows (Mickey's Philharmagic, Honey I Shrunk the Audience, It's Tough to be a Bug, and Muppets 4-D).
The outdoor shows, of course, are not air conditioned. That includes Indiana Jones, Beauty and the Beast, Festival of the Lion King, Tarzan Rocks. These shows have giant mister fans blowing over the rows of seats on really hot days.