You have 2 choices
1) you can do a query for all of the posts in the CPT, loop through them and count the check boxes
2) You can do an individual query for each of the 4 values. See the section titled 3. Multiple custom field values (array based values) on this page https://www.advancedcustomfields.com/resources/query-posts-custom-fields/. (Checkboxes are stored as arrays.)
