In the following example on a vanilla instance of core 2.6.4+ with "exclude hidden items from totals" set on the course, I created two categories (aggregation set to Sum of Grades), each with two 100-point items, and gave the student 100 points for each item (400 total points). I then hid item 4 which should change the totals to 300/300.

Gradebook Testing
Category 1
Item 1 100.00 0–100 100.00 %
Item 2 100.00 0–100 100.00 %
Category total 200.00 0–200 100.00 %

Category 2
Item 3 100.00 0–100 100.00 %
Item 4 (hid) - 0–100 -
Category total 100.00 0–100 200.00 %

Course total 200.00 0–200 200.00 %

As you can see from the results, the hidden item results in the course total of 200 points (and 200%), and Category 2 has the wrong percentage.