So only by looking at the names in chars and crossing with the select menu :
select menu : 49 empty out of 120 chars places -> 71 chars displayed
in the folder : 71 chars folders
but a difference : folder : g-makagi | no !universe
Select menu : no g-makagi | !universe
(maybe it's the same character but idk)
I'm sorry but i don't know all chars who are on your screenshot so i can't tell you who are missing
as for the datas inside of the chars folders i don't know how mugen works so i can't help you for that neither sorry.