In the previous version Madrid, a category with inactive items or if those items had the checkbox "hide on portal" checked, the associated categories and parent categories wouldn't display in the portal.
In Orlando, even if you have no active or displayable items inside a category, this category and parent categories will still appear.
The instance option of the SC Categories 'omit badges' is checked by default out of box. As we faced performance issues, since Orlando we don't calculate the items count when 'omit badges' is checked.
As a workaround and if you still want to hide the categories and sub-categories then you can uncheck the 'omitbadges' option.