They didn't fill the tubes with compressed air to offset the weight of the torpedo. Air weighs a lot less than water, so using air to offset the weight wouldn't work. Compressed air from a special tank was used to fire the torpedo. They then shut the outer door and used the compressed air to force the water out of the tube so they could open the inner door to reload it.
http://www.maritime.org/fleetsub/tubes/chap9.htm