You can manage your SD card better, or use one of following options:
From
http://wiki.gbatemp.net/wiki/AKAIO#Globalsettings.ini
hiddenFileNames = __aio,__ak2,__rpg,akmenu4.nds,moonshl2,adult_e-book.txt
Add files or folders to this list that you wish to have hidden from view. The list must be comma delimited with no spaces between entries. Additionally, make sure that all folder and file names are written in lower case letters, even if the actual folder or file name contains an upper case letter. File extenison listing is not supported, all files must be listed by their full name.
or
showHiddenFiles = 0
Allows AKAIO to display files which have their hidden attribute enabled. Folders and files listed in the hiddenFileNames option will never be displayed.
I would recommend you use the first option since the default option for XP Explorer is to not show hidden files/folders.