I haven't seen the Villain's show yet, but all the other shows I've seen in the Walt Disney Theater - except the movies - run about 1 hour.
However, there's no need to worry about skipping the show for the Pirate night or vice versa. They have the evenings scheduled such that everyone can attend dinner, the show and make it to the pirate party. You might not get the best spot, but there's usually plenty of space to watch the festivities (at least on the Magic and Wonder).