Currently a teacher can go to the "Categories and Items" page and hide a category containing assessment items. All of the items will be hidden which makes sense. The teacher can then manually make some of the items visible and the category remains invisible.
This conflict of an invisible category containing a visible item leads to some strange behaviour. The invisible category means the item won't be displayed to students on the user report but it appears that the visible, yet not displayed, item is still included in aggregation calculations. To fix that the teacher needs to show the category which then automatically shows everything else in that category so they then have to go through and hide everything but the one item they originally marked visible. Plus it's just generally illogical to to have a visible item in an invisible category.
When an item is made visible that should propagate up to its category.