Data displayed as a check box is just that. Checkbox is a UI item and doesn't effect the table storage of your data. You can count the "Yes"s the same way you would for any other field value.
A couple of options include searching for "Yes" and getting the record count (by hand or via script) or you could use related records and calculation fields.
Assuming that the checkbox holds either "Yes" or is empty, you can use a summary field Count of: checkboxField.
Be aware that this reflects the found set, so to get a result across all records, show all records.