Jumping onto the ground is generally discouraged while canyoneering because jumping has led to a lot of leg and ankle injuries and groups that have needed rescueing. Even if you don't need rescueing, it really sucks to have to finish a canyon and an exit hike with a sprained ankle! Because of this, jumping is considered bad form in the sport.
Jumping into water, on the other hand, is a very useful skill when done correctly. Never jump into water of unknown depth! In pothole canyons, often the most efficient way to proceed through a canyon is to meat anchor one person down. That person checks the water depth all around and checks for protruding rocks and ledges. If the water is deep enough, the rest of the group can jump, saving time by not rappelling. If the water is not deep enough, the people up top can set a more permanent anchor and rappel down.