Actually, both actors were indeed completely pantsless all throughout all scenes on both the blimp and the biplane, and throughout much of the rest of the movie as well, including all the long shots of Ford and Connery running on the beach, the entire tank chase, and the first half of the motorcycle chase; ILM then added special pants effects throughout these scenes where necessary.
For most such shots in this not-quite-fully-digital age, painstakingly crafted miniature pants made of malleable material were stop-motion animated against projected backgrounds of the live-action plates, so that the pants could be matched against the actors' leg positions as closely as possible. Sometimes, as soon as the animator finished adjusting the pants puppet(s) for each frame, the projected live-action background was replaced with bluescreen, the frame exposed, and then the live-action plate reinserted for the animator's reference for the next adjustment; these shots were then optically composited in the usual manner with the live-action plates. For other shots, the projected backgrounds were actually used right with the pants miniatures in front, so that the final shot included live-action photography that hadn't gone through as many generations of reproduction, to retain greater photographic detail.
Additional pants effects were added to many of the background extras in the Venice street / canal sequences to replace the clearly visible officially licensed Indiana Jones underwear many of them insisted upon wearing on the outside of their jeans, as well as to John Williams in some of the behind-the-scenes documentary footage, as he actually attended most of the scoring sessions wearing nothing on his legs but boxer shorts signed by Cole Porter and Benny Goodman.