In any major Juju version change, we take the opportunity to add significant new functionality, which sometimes mean breaking compatibility. To help ease the transition, the Juju 2.9 CLI client is compatible with 2.9 and 3.0 controllers, so you can use that until your scripts are updated.
The CLI changes you refer to are for actions - he’s an earlier post explaining the new features. In 2.9 or earlier, it was opt in. In 3.0, the new behaviour becomes the default.