In Novelcrafter, you can only delete empty items (chapters/acts). To preserve your work, scenes are always archived, so that you can later recover the work.
To archive a scene
To archive a scene, click on the scene action menu (three vertical dots), and at the bottom of the menu is the archive scene option.
You can find more information on recovering an archived scene here.
If there is no text in the summary or scene, then instead the option to delete the scene will appear.
To delete a chapter
If a chapter has a scene with content in it, then it cannot be deleted - you need to first archive the composite scenes (see above).
Once you have an "empty" chapter, the option to delete the chapter will be present in the chapter action menu (three dots).
To delete an act
Likewise, if there chapters with content within an act, you cannot delete the act.
Once the populated scenes are archived, clicking on the act action menu will show the option to delete the act. In the image below, both chapters/scenes are empty, with no text or summary, hence we can delete the act.