Here's how you can delete Labels you don't need in your simulation:
Go to Data and Rules> Central Label Editor and click on "Erase" all its Actions.

Apart from Actions, a Label might be used by other features such as Visual Logic or Distributions. Simul8 will point you to the name of the feature (e.g. Visual Logic Section 1), so you can decide whether to stop using the Label for this feature or not, before deleting it.