Yes, this is a "missing link" of WordPress.

Default true for categories, but filterable (BC implications).
Default off for tags, but filterable.
Off for post formats.
Off for nav_menu (name for classic nav menus)
New boolean property for registering custom taxonomies, default to value of public && hierarchical (BC implications).

Users should have a status, so when not empty, behave like having no capabilities (like customer role on WC). Initial status as an option. Plugins can easily define their own and how that will affect real caps.

Next: Taxonomy terms should resemble posts further, like have a status [ draft, publish, private, archived]. (draft = can be added, publicly invisible, archived = cannot be added, publicly visible), or something like that.